SIGSCANLIG documentation


 

CONTENTS

1.0 SUMMARY
2.0 INPUTS & OUTPUTS
3.0 INPUT FILE FORMAT
4.0 OUTPUT FILE FORMAT
5.0 DATA FILES
6.0 USAGE
7.0 KNOWN BUGS & WARNINGS
8.0 NOTES
9.0 DESCRIPTION
10.0 ALGORITHM
11.0 RELATED APPLICATIONS
12.0 DIAGNOSTIC ERROR MESSAGES
13.0 AUTHORS
14.0 REFERENCES



1.0 SUMMARY

Searches ligand-signature library and writes hits (LHF file)

Generates LHF files (ligand hits file) of hits from scanning sequences against a library of ligand-binding signatures.


2.0 INPUTS & OUTPUTS

SIGSCANLIG reads one more sequences, e.g. from a sequence database, and scans each in turn against a library of ligand-binding signatures (directory of signature files). The signatures may be of type 1D or 3D. To perform the scan, the user provides a scoring matrix which is either a residue substitution matrix (1D signatures) or matrix of 3D:1D (environment:residue) scores (3D). Various other parameters including gap insertion and extension penalties and a score mode are also set. For each query sequence, 3 files are generated as follows: (i) An LHF file (ligand hits file) of hits to the signatures. (ii) A SAF file (signature alignment file) of the corresponding signature-sequence alignments. (iii) A results file, containing a list of hits (ligands), rank-ordered on the basis of score. The user specifies the query sequences and also the paths of the signature files (input), LHF, SAF and results files (output). The file extensions are specified in the ACD file.


3.0 INPUT FILE FORMAT

The format of the signature file is described in SIGGEN documentation (1D signatures) and the SIGGENLIG documentation (3D signatures).
SIGSCANLIG can read protein sequences in any sequence format supported by EMBOSS.

Input files for usage example

File: swtiny

> Q9WVI4^.^516^664^.^55074^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^Adenylyl and guanylyl cyclase catalytic domain^Adenylyl and guanylyl cyclase catalytic domain^PSIBLAST^84.40^0.000e+00^2.000e-16
DDVTMLFSDIVGFTAICAQCTPMQVISMLNELYTRFDHQCGFLDIYKVETIGDAYCVASG
LHRKSLCHAKPIALMALKMMELSEEVLTPDGRPIQMRIGIHSGSVLAGVVGVRMPRYCLF
GNNVTLASKFESGSHPRRINISPTTYQLL
> Q9ERL9^.^480^631^.^55074^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^Adenylyl and guanylyl cyclase catalytic domain^Adenylyl and guanylyl cyclase catalytic domain^PSIBLAST^72.10^0.000e+00^1.000e-12
VTMLFSDIVGFTAICSQCSPLQVITMLNALYTRFDQQCGELDVYKVETIGDAYCVAGGLH
RESDTHAVQIALMALKMMELSNEVMSPHGEPIKMRIGLHSGSVFAGVVGVKMPRYCLFGN
NVTLANKFESCSVPRKINVSPTTYRLLKDCPG
> Q9DGG6^.^380^560^.^55074^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^Adenylyl and guanylyl cyclase catalytic domain^Adenylyl and guanylyl cyclase catalytic domain^PSIBLAST^142.00^0.000e+00^8.000e-34
EQVSILFADIVGFTKMSANKSAHALVGLLNDLFGRFDRLCEDTKCEKISTLGDCYYCVAG
CPEPRADHAYCCIEMGLGMIKAIEQFCQEKKEMVNMRVGVHTGTVLCGILGMRRFKFDVW
SNDVNLANLMEQLGVAGKVHISEATAKYLDDRYEMEDGKVTERVGQSAVADQLKGLKTYL
I
> Q99396^.^262^473^.^55074^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^Adenylyl and guanylyl cyclase catalytic domain^Adenylyl and guanylyl cyclase catalytic domain^PSIBLAST^192.00^0.000e+00^0.000e+00
KELADPVTLIFTDIESSTAQWATQPELMPDAVATHHSMVRSLIENYDCYEVKTVGDSFMI
ACKSPFAAVQLAQELQLRFLRLDWGTTVFDEFYREFEERHAEEGDGKYKPPTARLDPEVY
RQLWNGLRVRVGIHTGLCDIRYDEVTKGYDYYGQTANTAARTESVGNGGQVLMTCETYHS
LSTAERSQFDVTPLGGVPLRGVSEPVEVYQLN




4.0 OUTPUT FILE FORMAT

LHF file (ligand hits file)
Each LHF file contains the hits from the search of a single query sequence against the library of signatures. The file (Figure 1) contains two lines per hit. The first contains a description of the hit in 17 text tokens delimited by '^'. The second line contains the protein sequence. The tokens are as follows (a '.' is given where a token does not have a value).
The next 9 tokens refer to the domain family, superfamily etc for which the signature was derived and are as follows:
The next 3 tokens refer to the hit, specifically, information about the search result as follows:

SAF file (signature alignment file)
The format of the SAF file (signature alignment file, Figure 2) is more or less identical to DAF (domain alignment file) described in the DOMAINALIGN documentation. The file conforms to EMBOSS "simple" multiple sequence alignment format. Each file contains the signature-sequence alignments corresponding to the search of a single query sequence against a library of signatures. The SAF file generated by SIGSCANLIG contains some unique features which are summarised here.

All lines beginning with '#' are comments and the first line is always '# DE Alignment of query sequence against library of signatures'. Each signature-sequence alignment is contained in one or more blocks in the file. These blocks are preceeded by a comment line containing information for the corresponding hit from the LHF (above). Each block contains contains the signature identifier code and accession number of the protein sequence, sequence positions and a section of the signature-sequence alignment.

Results file
Each results file (Figure 3) contains the summarised results of the search of a single query sequence against the library of signatures. The results file contains a list of ligands, rank-ordered on the basis of score (highest-scoring ligand is given first). There are four columns under the labels 'LIGID, 'PATCHES', 'SITES' and 'SCORE'. These give the ligand identifier, the number of patches for that ligand binding site, the number of sites for the ligand and the score of the sequence-signature match. In the example shown (Figure 3) there is a single ligand. Typically, the library would represent all ligands represented in PDB.

Figure 3 Excerpt from a results file (output)
LIGID     PATCHES   SITES     SCORE     
101       0         1         0.48      

Output files for usage example

Directory: lhf

This directory contains output files, for example Q99396^.^262^473^.^55074^Alpha.lhf Q9DGG6^.^380^560^.^55074^Alpha.lhf Q9ERL9^.^480^631^.^55074^Alpha.lhf and Q9WVI4^.^516^664^.^55074^Alpha.lhf.

File: lhf/Q99396^.^262^473^.^55074^Alpha.lhf

> Q99396^.^262^473^.^55074^Alpha^.^99^138^LIGAND^1ii7;^d1ii7a_^101^2^2^0^0^1DF^7.00^0.000e+00^0.000e+00
KELADPVTLIFTDIESSTAQWATQPELMPDAVATHHSMVRSLIENYDCYEVKTVGDSFMIACKSPFAAVQLAQELQLRFLRLDWGTTVFDEFYREFEERHAEEGDGKYKPPTARLDPEVYRQLWNGLRVRVGIHTGLCDIRYDEVTKGYDYYGQTANTAARTESVGNGGQVLMTCETYHSLSTAERSQFDVTPLGGVPLRGVSEPVEVYQLN
> Q99396^.^262^473^.^55074^Alpha^.^97^138^LIGAND^1ii7;^d1ii7a_^MN^1^1^0^0^1DF^5.33^0.000e+00^0.000e+00
KELADPVTLIFTDIESSTAQWATQPELMPDAVATHHSMVRSLIENYDCYEVKTVGDSFMIACKSPFAAVQLAQELQLRFLRLDWGTTVFDEFYREFEERHAEEGDGKYKPPTARLDPEVYRQLWNGLRVRVGIHTGLCDIRYDEVTKGYDYYGQTANTAARTESVGNGGQVLMTCETYHSLSTAERSQFDVTPLGGVPLRGVSEPVEVYQLN
> Q99396^.^262^473^.^55074^Alpha^.^130^210^LIGAND^2hhb;^.^PO4^1^1^0^0^1DF^4.00^0.000e+00^0.000e+00
KELADPVTLIFTDIESSTAQWATQPELMPDAVATHHSMVRSLIENYDCYEVKTVGDSFMIACKSPFAAVQLAQELQLRFLRLDWGTTVFDEFYREFEERHAEEGDGKYKPPTARLDPEVYRQLWNGLRVRVGIHTGLCDIRYDEVTKGYDYYGQTANTAARTESVGNGGQVLMTCETYHSLSTAERSQFDVTPLGGVPLRGVSEPVEVYQLN
> Q99396^.^262^473^.^55074^Alpha^.^12^17^LIGAND^1cs4;^d1cs4a_^POP^1^1^0^0^1DF^3.00^0.000e+00^0.000e+00
KELADPVTLIFTDIESSTAQWATQPELMPDAVATHHSMVRSLIENYDCYEVKTVGDSFMIACKSPFAAVQLAQELQLRFLRLDWGTTVFDEFYREFEERHAEEGDGKYKPPTARLDPEVYRQLWNGLRVRVGIHTGLCDIRYDEVTKGYDYYGQTANTAARTESVGNGGQVLMTCETYHSLSTAERSQFDVTPLGGVPLRGVSEPVEVYQLN
> Q99396^.^262^473^.^55074^Alpha^.^12^56^LIGAND^1cs4;^d1cs4a_^MG^1^1^0^0^1DF^2.00^0.000e+00^0.000e+00
KELADPVTLIFTDIESSTAQWATQPELMPDAVATHHSMVRSLIENYDCYEVKTVGDSFMIACKSPFAAVQLAQELQLRFLRLDWGTTVFDEFYREFEERHAEEGDGKYKPPTARLDPEVYRQLWNGLRVRVGIHTGLCDIRYDEVTKGYDYYGQTANTAARTESVGNGGQVLMTCETYHSLSTAERSQFDVTPLGGVPLRGVSEPVEVYQLN
> Q99396^.^262^473^.^55074^Alpha^.^11^55^LIGAND^1cs4;^d1cs4a_^101^1^2^0^0^1DF^1.83^0.000e+00^0.000e+00
KELADPVTLIFTDIESSTAQWATQPELMPDAVATHHSMVRSLIENYDCYEVKTVGDSFMIACKSPFAAVQLAQELQLRFLRLDWGTTVFDEFYREFEERHAEEGDGKYKPPTARLDPEVYRQLWNGLRVRVGIHTGLCDIRYDEVTKGYDYYGQTANTAARTESVGNGGQVLMTCETYHSLSTAERSQFDVTPLGGVPLRGVSEPVEVYQLN
> Q99396^.^262^473^.^55074^Alpha^.^16^126^LIGAND^2hhb;^.^HEM^4^4^0^0^1DF^1.00^0.000e+00^0.000e+00
KELADPVTLIFTDIESSTAQWATQPELMPDAVATHHSMVRSLIENYDCYEVKTVGDSFMIACKSPFAAVQLAQELQLRFLRLDWGTTVFDEFYREFEERHAEEGDGKYKPPTARLDPEVYRQLWNGLRVRVGIHTGLCDIRYDEVTKGYDYYGQTANTAARTESVGNGGQVLMTCETYHSLSTAERSQFDVTPLGGVPLRGVSEPVEVYQLN
> Q99396^.^262^473^.^55074^Alpha^.^32^126^LIGAND^2hhb;^.^HEM^1^4^0^0^1DF^0.94^0.000e+00^0.000e+00
KELADPVTLIFTDIESSTAQWATQPELMPDAVATHHSMVRSLIENYDCYEVKTVGDSFMIACKSPFAAVQLAQELQLRFLRLDWGTTVFDEFYREFEERHAEEGDGKYKPPTARLDPEVYRQLWNGLRVRVGIHTGLCDIRYDEVTKGYDYYGQTANTAARTESVGNGGQVLMTCETYHSLSTAERSQFDVTPLGGVPLRGVSEPVEVYQLN
> Q99396^.^262^473^.^55074^Alpha^.^22^126^LIGAND^2hhb;^.^HEM^3^4^0^0^1DF^0.74^0.000e+00^0.000e+00
KELADPVTLIFTDIESSTAQWATQPELMPDAVATHHSMVRSLIENYDCYEVKTVGDSFMIACKSPFAAVQLAQELQLRFLRLDWGTTVFDEFYREFEERHAEEGDGKYKPPTARLDPEVYRQLWNGLRVRVGIHTGLCDIRYDEVTKGYDYYGQTANTAARTESVGNGGQVLMTCETYHSLSTAERSQFDVTPLGGVPLRGVSEPVEVYQLN
> Q99396^.^262^473^.^55074^Alpha^.^16^126^LIGAND^2hhb;^.^HEM^2^4^0^0^1DF^0.59^0.000e+00^0.000e+00
KELADPVTLIFTDIESSTAQWATQPELMPDAVATHHSMVRSLIENYDCYEVKTVGDSFMIACKSPFAAVQLAQELQLRFLRLDWGTTVFDEFYREFEERHAEEGDGKYKPPTARLDPEVYRQLWNGLRVRVGIHTGLCDIRYDEVTKGYDYYGQTANTAARTESVGNGGQVLMTCETYHSLSTAERSQFDVTPLGGVPLRGVSEPVEVYQLN
> Q99396^.^262^473^.^55074^Alpha^.^0^0^LIGAND^1cs4;^d1cs4a_^FOK^1^1^0^0^1DF^-1000000.00^0.000e+00^0.000e+00
KELADPVTLIFTDIESSTAQWATQPELMPDAVATHHSMVRSLIENYDCYEVKTVGDSFMIACKSPFAAVQLAQELQLRFLRLDWGTTVFDEFYREFEERHAEEGDGKYKPPTARLDPEVYRQLWNGLRVRVGIHTGLCDIRYDEVTKGYDYYGQTANTAARTESVGNGGQVLMTCETYHSLSTAERSQFDVTPLGGVPLRGVSEPVEVYQLN

File: lhf/Q9DGG6^.^380^560^.^55074^Alpha.lhf

> Q9DGG6^.^380^560^.^55074^Alpha^.^8^52^LIGAND^1cs4;^d1cs4a_^101^1^2^0^0^1DF^5.50^0.000e+00^0.000e+00
EQVSILFADIVGFTKMSANKSAHALVGLLNDLFGRFDRLCEDTKCEKISTLGDCYYCVAGCPEPRADHAYCCIEMGLGMIKAIEQFCQEKKEMVNMRVGVHTGTVLCGILGMRRFKFDVWSNDVNLANLMEQLGVAGKVHISEATAKYLDDRYEMEDGKVTERVGQSAVADQLKGLKTYLI
> Q9DGG6^.^380^560^.^55074^Alpha^.^8^52^LIGAND^1cs4;^d1cs4a_^MG^1^1^0^0^1DF^5.50^0.000e+00^0.000e+00
EQVSILFADIVGFTKMSANKSAHALVGLLNDLFGRFDRLCEDTKCEKISTLGDCYYCVAGCPEPRADHAYCCIEMGLGMIKAIEQFCQEKKEMVNMRVGVHTGTVLCGILGMRRFKFDVWSNDVNLANLMEQLGVAGKVHISEATAKYLDDRYEMEDGKVTERVGQSAVADQLKGLKTYLI
> Q9DGG6^.^380^560^.^55074^Alpha^.^8^13^LIGAND^1cs4;^d1cs4a_^POP^1^1^0^0^1DF^4.17^0.000e+00^0.000e+00
EQVSILFADIVGFTKMSANKSAHALVGLLNDLFGRFDRLCEDTKCEKISTLGDCYYCVAGCPEPRADHAYCCIEMGLGMIKAIEQFCQEKKEMVNMRVGVHTGTVLCGILGMRRFKFDVWSNDVNLANLMEQLGVAGKVHISEATAKYLDDRYEMEDGKVTERVGQSAVADQLKGLKTYLI
> Q9DGG6^.^380^560^.^55074^Alpha^.^99^179^LIGAND^2hhb;^.^PO4^1^1^0^0^1DF^4.00^0.000e+00^0.000e+00
EQVSILFADIVGFTKMSANKSAHALVGLLNDLFGRFDRLCEDTKCEKISTLGDCYYCVAGCPEPRADHAYCCIEMGLGMIKAIEQFCQEKKEMVNMRVGVHTGTVLCGILGMRRFKFDVWSNDVNLANLMEQLGVAGKVHISEATAKYLDDRYEMEDGKVTERVGQSAVADQLKGLKTYLI
> Q9DGG6^.^380^560^.^55074^Alpha^.^100^139^LIGAND^1ii7;^d1ii7a_^101^2^2^0^0^1DF^3.50^0.000e+00^0.000e+00
EQVSILFADIVGFTKMSANKSAHALVGLLNDLFGRFDRLCEDTKCEKISTLGDCYYCVAGCPEPRADHAYCCIEMGLGMIKAIEQFCQEKKEMVNMRVGVHTGTVLCGILGMRRFKFDVWSNDVNLANLMEQLGVAGKVHISEATAKYLDDRYEMEDGKVTERVGQSAVADQLKGLKTYLI
> Q9DGG6^.^380^560^.^55074^Alpha^.^20^61^LIGAND^1ii7;^d1ii7a_^MN^1^1^0^0^1DF^2.33^0.000e+00^0.000e+00
EQVSILFADIVGFTKMSANKSAHALVGLLNDLFGRFDRLCEDTKCEKISTLGDCYYCVAGCPEPRADHAYCCIEMGLGMIKAIEQFCQEKKEMVNMRVGVHTGTVLCGILGMRRFKFDVWSNDVNLANLMEQLGVAGKVHISEATAKYLDDRYEMEDGKVTERVGQSAVADQLKGLKTYLI
> Q9DGG6^.^380^560^.^55074^Alpha^.^74^178^LIGAND^2hhb;^.^HEM^3^4^0^0^1DF^1.00^0.000e+00^0.000e+00
EQVSILFADIVGFTKMSANKSAHALVGLLNDLFGRFDRLCEDTKCEKISTLGDCYYCVAGCPEPRADHAYCCIEMGLGMIKAIEQFCQEKKEMVNMRVGVHTGTVLCGILGMRRFKFDVWSNDVNLANLMEQLGVAGKVHISEATAKYLDDRYEMEDGKVTERVGQSAVADQLKGLKTYLI
> Q9DGG6^.^380^560^.^55074^Alpha^.^84^178^LIGAND^2hhb;^.^HEM^1^4^0^0^1DF^0.82^0.000e+00^0.000e+00
EQVSILFADIVGFTKMSANKSAHALVGLLNDLFGRFDRLCEDTKCEKISTLGDCYYCVAGCPEPRADHAYCCIEMGLGMIKAIEQFCQEKKEMVNMRVGVHTGTVLCGILGMRRFKFDVWSNDVNLANLMEQLGVAGKVHISEATAKYLDDRYEMEDGKVTERVGQSAVADQLKGLKTYLI
> Q9DGG6^.^380^560^.^55074^Alpha^.^68^178^LIGAND^2hhb;^.^HEM^2^4^0^0^1DF^0.65^0.000e+00^0.000e+00
EQVSILFADIVGFTKMSANKSAHALVGLLNDLFGRFDRLCEDTKCEKISTLGDCYYCVAGCPEPRADHAYCCIEMGLGMIKAIEQFCQEKKEMVNMRVGVHTGTVLCGILGMRRFKFDVWSNDVNLANLMEQLGVAGKVHISEATAKYLDDRYEMEDGKVTERVGQSAVADQLKGLKTYLI
> Q9DGG6^.^380^560^.^55074^Alpha^.^68^178^LIGAND^2hhb;^.^HEM^4^4^0^0^1DF^0.47^0.000e+00^0.000e+00
EQVSILFADIVGFTKMSANKSAHALVGLLNDLFGRFDRLCEDTKCEKISTLGDCYYCVAGCPEPRADHAYCCIEMGLGMIKAIEQFCQEKKEMVNMRVGVHTGTVLCGILGMRRFKFDVWSNDVNLANLMEQLGVAGKVHISEATAKYLDDRYEMEDGKVTERVGQSAVADQLKGLKTYLI
> Q9DGG6^.^380^560^.^55074^Alpha^.^0^0^LIGAND^1cs4;^d1cs4a_^FOK^1^1^0^0^1DF^-1000000.00^0.000e+00^0.000e+00
EQVSILFADIVGFTKMSANKSAHALVGLLNDLFGRFDRLCEDTKCEKISTLGDCYYCVAGCPEPRADHAYCCIEMGLGMIKAIEQFCQEKKEMVNMRVGVHTGTVLCGILGMRRFKFDVWSNDVNLANLMEQLGVAGKVHISEATAKYLDDRYEMEDGKVTERVGQSAVADQLKGLKTYLI

File: lhf/Q9ERL9^.^480^631^.^55074^Alpha.lhf

> Q9ERL9^.^480^631^.^55074^Alpha^.^6^50^LIGAND^1cs4;^d1cs4a_^MG^1^1^0^0^1DF^5.50^0.000e+00^0.000e+00
VTMLFSDIVGFTAICSQCSPLQVITMLNALYTRFDQQCGELDVYKVETIGDAYCVAGGLHRESDTHAVQIALMALKMMELSNEVMSPHGEPIKMRIGLHSGSVFAGVVGVKMPRYCLFGNNVTLANKFESCSVPRKINVSPTTYRLLKDCPG
> Q9ERL9^.^480^631^.^55074^Alpha^.^6^50^LIGAND^1cs4;^d1cs4a_^101^1^2^0^0^1DF^5.17^0.000e+00^0.000e+00
VTMLFSDIVGFTAICSQCSPLQVITMLNALYTRFDQQCGELDVYKVETIGDAYCVAGGLHRESDTHAVQIALMALKMMELSNEVMSPHGEPIKMRIGLHSGSVFAGVVGVKMPRYCLFGNNVTLANKFESCSVPRKINVSPTTYRLLKDCPG
> Q9ERL9^.^480^631^.^55074^Alpha^.^98^137^LIGAND^1ii7;^d1ii7a_^101^2^2^0^0^1DF^4.50^0.000e+00^0.000e+00
VTMLFSDIVGFTAICSQCSPLQVITMLNALYTRFDQQCGELDVYKVETIGDAYCVAGGLHRESDTHAVQIALMALKMMELSNEVMSPHGEPIKMRIGLHSGSVFAGVVGVKMPRYCLFGNNVTLANKFESCSVPRKINVSPTTYRLLKDCPG
> Q9ERL9^.^480^631^.^55074^Alpha^.^6^11^LIGAND^1cs4;^d1cs4a_^POP^1^1^0^0^1DF^4.17^0.000e+00^0.000e+00
VTMLFSDIVGFTAICSQCSPLQVITMLNALYTRFDQQCGELDVYKVETIGDAYCVAGGLHRESDTHAVQIALMALKMMELSNEVMSPHGEPIKMRIGLHSGSVFAGVVGVKMPRYCLFGNNVTLANKFESCSVPRKINVSPTTYRLLKDCPG
> Q9ERL9^.^480^631^.^55074^Alpha^.^63^104^LIGAND^1ii7;^d1ii7a_^MN^1^1^0^0^1DF^4.00^0.000e+00^0.000e+00
VTMLFSDIVGFTAICSQCSPLQVITMLNALYTRFDQQCGELDVYKVETIGDAYCVAGGLHRESDTHAVQIALMALKMMELSNEVMSPHGEPIKMRIGLHSGSVFAGVVGVKMPRYCLFGNNVTLANKFESCSVPRKINVSPTTYRLLKDCPG
> Q9ERL9^.^480^631^.^55074^Alpha^.^22^102^LIGAND^2hhb;^.^PO4^1^1^0^0^1DF^2.50^0.000e+00^0.000e+00
VTMLFSDIVGFTAICSQCSPLQVITMLNALYTRFDQQCGELDVYKVETIGDAYCVAGGLHRESDTHAVQIALMALKMMELSNEVMSPHGEPIKMRIGLHSGSVFAGVVGVKMPRYCLFGNNVTLANKFESCSVPRKINVSPTTYRLLKDCPG
> Q9ERL9^.^480^631^.^55074^Alpha^.^4^114^LIGAND^2hhb;^.^HEM^4^4^0^0^1DF^0.60^0.000e+00^0.000e+00
VTMLFSDIVGFTAICSQCSPLQVITMLNALYTRFDQQCGELDVYKVETIGDAYCVAGGLHRESDTHAVQIALMALKMMELSNEVMSPHGEPIKMRIGLHSGSVFAGVVGVKMPRYCLFGNNVTLANKFESCSVPRKINVSPTTYRLLKDCPG
> Q9ERL9^.^480^631^.^55074^Alpha^.^25^119^LIGAND^2hhb;^.^HEM^1^4^0^0^1DF^0.29^0.000e+00^0.000e+00
VTMLFSDIVGFTAICSQCSPLQVITMLNALYTRFDQQCGELDVYKVETIGDAYCVAGGLHRESDTHAVQIALMALKMMELSNEVMSPHGEPIKMRIGLHSGSVFAGVVGVKMPRYCLFGNNVTLANKFESCSVPRKINVSPTTYRLLKDCPG
> Q9ERL9^.^480^631^.^55074^Alpha^.^12^122^LIGAND^2hhb;^.^HEM^2^4^0^0^1DF^0.24^0.000e+00^0.000e+00
VTMLFSDIVGFTAICSQCSPLQVITMLNALYTRFDQQCGELDVYKVETIGDAYCVAGGLHRESDTHAVQIALMALKMMELSNEVMSPHGEPIKMRIGLHSGSVFAGVVGVKMPRYCLFGNNVTLANKFESCSVPRKINVSPTTYRLLKDCPG
> Q9ERL9^.^480^631^.^55074^Alpha^.^15^119^LIGAND^2hhb;^.^HEM^3^4^0^0^1DF^0.21^0.000e+00^0.000e+00
VTMLFSDIVGFTAICSQCSPLQVITMLNALYTRFDQQCGELDVYKVETIGDAYCVAGGLHRESDTHAVQIALMALKMMELSNEVMSPHGEPIKMRIGLHSGSVFAGVVGVKMPRYCLFGNNVTLANKFESCSVPRKINVSPTTYRLLKDCPG
> Q9ERL9^.^480^631^.^55074^Alpha^.^0^0^LIGAND^1cs4;^d1cs4a_^FOK^1^1^0^0^1DF^-1000000.00^0.000e+00^0.000e+00
VTMLFSDIVGFTAICSQCSPLQVITMLNALYTRFDQQCGELDVYKVETIGDAYCVAGGLHRESDTHAVQIALMALKMMELSNEVMSPHGEPIKMRIGLHSGSVFAGVVGVKMPRYCLFGNNVTLANKFESCSVPRKINVSPTTYRLLKDCPG

File: lhf/Q9WVI4^.^516^664^.^55074^Alpha.lhf

> Q9WVI4^.^516^664^.^55074^Alpha^.^8^52^LIGAND^1cs4;^d1cs4a_^MG^1^1^0^0^1DF^5.50^0.000e+00^0.000e+00
DDVTMLFSDIVGFTAICAQCTPMQVISMLNELYTRFDHQCGFLDIYKVETIGDAYCVASGLHRKSLCHAKPIALMALKMMELSEEVLTPDGRPIQMRIGIHSGSVLAGVVGVRMPRYCLFGNNVTLASKFESGSHPRRINISPTTYQLL
> Q9WVI4^.^516^664^.^55074^Alpha^.^8^52^LIGAND^1cs4;^d1cs4a_^101^1^2^0^0^1DF^5.17^0.000e+00^0.000e+00
DDVTMLFSDIVGFTAICAQCTPMQVISMLNELYTRFDHQCGFLDIYKVETIGDAYCVASGLHRKSLCHAKPIALMALKMMELSEEVLTPDGRPIQMRIGIHSGSVLAGVVGVRMPRYCLFGNNVTLASKFESGSHPRRINISPTTYQLL
> Q9WVI4^.^516^664^.^55074^Alpha^.^100^139^LIGAND^1ii7;^d1ii7a_^101^2^2^0^0^1DF^4.50^0.000e+00^0.000e+00
DDVTMLFSDIVGFTAICAQCTPMQVISMLNELYTRFDHQCGFLDIYKVETIGDAYCVASGLHRKSLCHAKPIALMALKMMELSEEVLTPDGRPIQMRIGIHSGSVLAGVVGVRMPRYCLFGNNVTLASKFESGSHPRRINISPTTYQLL
> Q9WVI4^.^516^664^.^55074^Alpha^.^8^13^LIGAND^1cs4;^d1cs4a_^POP^1^1^0^0^1DF^4.17^0.000e+00^0.000e+00
DDVTMLFSDIVGFTAICAQCTPMQVISMLNELYTRFDHQCGFLDIYKVETIGDAYCVASGLHRKSLCHAKPIALMALKMMELSEEVLTPDGRPIQMRIGIHSGSVLAGVVGVRMPRYCLFGNNVTLASKFESGSHPRRINISPTTYQLL
> Q9WVI4^.^516^664^.^55074^Alpha^.^25^105^LIGAND^2hhb;^.^PO4^1^1^0^0^1DF^3.50^0.000e+00^0.000e+00
DDVTMLFSDIVGFTAICAQCTPMQVISMLNELYTRFDHQCGFLDIYKVETIGDAYCVASGLHRKSLCHAKPIALMALKMMELSEEVLTPDGRPIQMRIGIHSGSVLAGVVGVRMPRYCLFGNNVTLASKFESGSHPRRINISPTTYQLL
> Q9WVI4^.^516^664^.^55074^Alpha^.^43^84^LIGAND^1ii7;^d1ii7a_^MN^1^1^0^0^1DF^3.33^0.000e+00^0.000e+00
DDVTMLFSDIVGFTAICAQCTPMQVISMLNELYTRFDHQCGFLDIYKVETIGDAYCVASGLHRKSLCHAKPIALMALKMMELSEEVLTPDGRPIQMRIGIHSGSVLAGVVGVRMPRYCLFGNNVTLASKFESGSHPRRINISPTTYQLL
> Q9WVI4^.^516^664^.^55074^Alpha^.^27^121^LIGAND^2hhb;^.^HEM^1^4^0^0^1DF^0.53^0.000e+00^0.000e+00
DDVTMLFSDIVGFTAICAQCTPMQVISMLNELYTRFDHQCGFLDIYKVETIGDAYCVASGLHRKSLCHAKPIALMALKMMELSEEVLTPDGRPIQMRIGIHSGSVLAGVVGVRMPRYCLFGNNVTLASKFESGSHPRRINISPTTYQLL
> Q9WVI4^.^516^664^.^55074^Alpha^.^17^121^LIGAND^2hhb;^.^HEM^3^4^0^0^1DF^0.42^0.000e+00^0.000e+00
DDVTMLFSDIVGFTAICAQCTPMQVISMLNELYTRFDHQCGFLDIYKVETIGDAYCVASGLHRKSLCHAKPIALMALKMMELSEEVLTPDGRPIQMRIGIHSGSVLAGVVGVRMPRYCLFGNNVTLASKFESGSHPRRINISPTTYQLL
> Q9WVI4^.^516^664^.^55074^Alpha^.^6^116^LIGAND^2hhb;^.^HEM^4^4^0^0^1DF^0.33^0.000e+00^0.000e+00
DDVTMLFSDIVGFTAICAQCTPMQVISMLNELYTRFDHQCGFLDIYKVETIGDAYCVASGLHRKSLCHAKPIALMALKMMELSEEVLTPDGRPIQMRIGIHSGSVLAGVVGVRMPRYCLFGNNVTLASKFESGSHPRRINISPTTYQLL
> Q9WVI4^.^516^664^.^55074^Alpha^.^14^124^LIGAND^2hhb;^.^HEM^2^4^0^0^1DF^0.18^0.000e+00^0.000e+00
DDVTMLFSDIVGFTAICAQCTPMQVISMLNELYTRFDHQCGFLDIYKVETIGDAYCVASGLHRKSLCHAKPIALMALKMMELSEEVLTPDGRPIQMRIGIHSGSVLAGVVGVRMPRYCLFGNNVTLASKFESGSHPRRINISPTTYQLL
> Q9WVI4^.^516^664^.^55074^Alpha^.^0^0^LIGAND^1cs4;^d1cs4a_^FOK^1^1^0^0^1DF^-1000000.00^0.000e+00^0.000e+00
DDVTMLFSDIVGFTAICAQCTPMQVISMLNELYTRFDHQCGFLDIYKVETIGDAYCVASGLHRKSLCHAKPIALMALKMMELSEEVLTPDGRPIQMRIGIHSGSVLAGVVGVRMPRYCLFGNNVTLASKFESGSHPRRINISPTTYQLL

Directory: aln

This directory contains output files, for example Q99396^.^262^473^.^55074^Alpha.aln Q9DGG6^.^380^560^.^55074^Alpha.aln Q9ERL9^.^480^631^.^55074^Alpha.aln and Q9WVI4^.^516^664^.^55074^Alpha.aln.

File: aln/Q99396^.^262^473^.^55074^Alpha.aln

# DE   Alignment of query sequence against library of signatures
# XX
# > Q99396^.^262^473^.^55074^Alpha^.^99^138^LIGAND^1ii7;^d1ii7a_^101^2^2^0^0^1DF^7.00^0.000e+00^0.000e+00
# XX
Q99396^.^262^473^.^55074^Alpha1      KELADPVTLIFTDIESSTAQWATQPELMPDAVATHHSMVRSLIEN 45
101_2_0           -      ---------------------------------------------
Q99396^.^262^473^.^55074^Alpha46     YDCYEVKTVGDSFMIACKSPFAAVQLAQELQLRFLRLDWGTTVFD 90
101_2_0           -      ---------------------------------------------
Q99396^.^262^473^.^55074^Alpha91     EFYREFEERHAEEGDGKYKPPTARLDPEVYRQLWNGLRVRVGIHT 135
101_2_0           -      ---------*-----------------------------------
Q99396^.^262^473^.^55074^Alpha136    GLCDIRYDEVTKGYDYYGQTANTAARTESVGNGGQVLMTCETYHS 180
101_2_0           -      ---*-----------------------------------------
Q99396^.^262^473^.^55074^Alpha181    LSTAERSQFDVTPLGGVPLRGVSEPVEVYQLN              225
101_2_0           -      --------------------------------             
# XX
# > Q99396^.^262^473^.^55074^Alpha^.^97^138^LIGAND^1ii7;^d1ii7a_^MN^1^1^0^0^1DF^5.33^0.000e+00^0.000e+00
# XX
Q99396^.^262^473^.^55074^Alpha1      KELADPVTLIFTDIESSTAQWATQPELMPDAVATHHSMVRSLIEN 45
MN_1_0            -      ---------------------------------------------
Q99396^.^262^473^.^55074^Alpha46     YDCYEVKTVGDSFMIACKSPFAAVQLAQELQLRFLRLDWGTTVFD 90
MN_1_0            -      ---------------------------------------------
Q99396^.^262^473^.^55074^Alpha91     EFYREFEERHAEEGDGKYKPPTARLDPEVYRQLWNGLRVRVGIHT 135
MN_1_0            -      -------*-*-----------------------------------
Q99396^.^262^473^.^55074^Alpha136    GLCDIRYDEVTKGYDYYGQTANTAARTESVGNGGQVLMTCETYHS 180
MN_1_0            -      ---*-----------------------------------------
Q99396^.^262^473^.^55074^Alpha181    LSTAERSQFDVTPLGGVPLRGVSEPVEVYQLN              225
MN_1_0            -      --------------------------------             
# XX
# > Q99396^.^262^473^.^55074^Alpha^.^130^210^LIGAND^2hhb;^.^PO4^1^1^0^0^1DF^4.00^0.000e+00^0.000e+00
# XX
Q99396^.^262^473^.^55074^Alpha1      KELADPVTLIFTDIESSTAQWATQPELMPDAVATHHSMVRSLIEN 45
PO4_1_0           -      ---------------------------------------------
Q99396^.^262^473^.^55074^Alpha46     YDCYEVKTVGDSFMIACKSPFAAVQLAQELQLRFLRLDWGTTVFD 90
PO4_1_0           -      ---------------------------------------------
Q99396^.^262^473^.^55074^Alpha91     EFYREFEERHAEEGDGKYKPPTARLDPEVYRQLWNGLRVRVGIHT 135
PO4_1_0           -      ----------------------------------------*----
Q99396^.^262^473^.^55074^Alpha136    GLCDIRYDEVTKGYDYYGQTANTAARTESVGNGGQVLMTCETYHS 180
PO4_1_0           -      ---------------------------------------------
Q99396^.^262^473^.^55074^Alpha181    LSTAERSQFDVTPLGGVPLRGVSEPVEVYQLN              225
PO4_1_0           -      ------------------------------*-             
# XX
# > Q99396^.^262^473^.^55074^Alpha^.^12^17^LIGAND^1cs4;^d1cs4a_^POP^1^1^0^0^1DF^3.00^0.000e+00^0.000e+00
# XX
Q99396^.^262^473^.^55074^Alpha1      KELADPVTLIFTDIESSTAQWATQPELMPDAVATHHSMVRSLIEN 45
POP_1_0           -      ------------******---------------------------
Q99396^.^262^473^.^55074^Alpha46     YDCYEVKTVGDSFMIACKSPFAAVQLAQELQLRFLRLDWGTTVFD 90
POP_1_0           -      ---------------------------------------------
Q99396^.^262^473^.^55074^Alpha91     EFYREFEERHAEEGDGKYKPPTARLDPEVYRQLWNGLRVRVGIHT 135
POP_1_0           -      ---------------------------------------------
Q99396^.^262^473^.^55074^Alpha136    GLCDIRYDEVTKGYDYYGQTANTAARTESVGNGGQVLMTCETYHS 180


  [Part of this file has been deleted for brevity]

# > Q99396^.^262^473^.^55074^Alpha^.^32^126^LIGAND^2hhb;^.^HEM^1^4^0^0^1DF^0.94^0.000e+00^0.000e+00
# XX
Q99396^.^262^473^.^55074^Alpha1      KELADPVTLIFTDIESSTAQWATQPELMPDAVATHHSMVRSLIEN 45
HEM_1_0           -      --------------------------------**-**--------
Q99396^.^262^473^.^55074^Alpha46     YDCYEVKTVGDSFMIACKSPFAAVQLAQELQLRFLRLDWGTTVFD 90
HEM_1_0           -      ---*--**--*-----------------*--**---*-*---**-
Q99396^.^262^473^.^55074^Alpha91     EFYREFEERHAEEGDGKYKPPTARLDPEVYRQLWNGLRVRVGIHT 135
HEM_1_0           -      -*----------------------------------*--------
Q99396^.^262^473^.^55074^Alpha136    GLCDIRYDEVTKGYDYYGQTANTAARTESVGNGGQVLMTCETYHS 180
HEM_1_0           -      ---------------------------------------------
Q99396^.^262^473^.^55074^Alpha181    LSTAERSQFDVTPLGGVPLRGVSEPVEVYQLN              225
HEM_1_0           -      --------------------------------             
# XX
# > Q99396^.^262^473^.^55074^Alpha^.^22^126^LIGAND^2hhb;^.^HEM^3^4^0^0^1DF^0.74^0.000e+00^0.000e+00
# XX
Q99396^.^262^473^.^55074^Alpha1      KELADPVTLIFTDIESSTAQWATQPELMPDAVATHHSMVRSLIEN 45
HEM_3_0           -      ----------------------*------*--**-**--------
Q99396^.^262^473^.^55074^Alpha46     YDCYEVKTVGDSFMIACKSPFAAVQLAQELQLRFLRLDWGTTVFD 90
HEM_3_0           -      ---*--**--*-----------------*--**---*-*---**-
Q99396^.^262^473^.^55074^Alpha91     EFYREFEERHAEEGDGKYKPPTARLDPEVYRQLWNGLRVRVGIHT 135
HEM_3_0           -      -*----------------------------------*--------
Q99396^.^262^473^.^55074^Alpha136    GLCDIRYDEVTKGYDYYGQTANTAARTESVGNGGQVLMTCETYHS 180
HEM_3_0           -      ---------------------------------------------
Q99396^.^262^473^.^55074^Alpha181    LSTAERSQFDVTPLGGVPLRGVSEPVEVYQLN              225
HEM_3_0           -      --------------------------------             
# XX
# > Q99396^.^262^473^.^55074^Alpha^.^16^126^LIGAND^2hhb;^.^HEM^2^4^0^0^1DF^0.59^0.000e+00^0.000e+00
# XX
Q99396^.^262^473^.^55074^Alpha1      KELADPVTLIFTDIESSTAQWATQPELMPDAVATHHSMVRSLIEN 45
HEM_2_0           -      ----------------*---------**-----------------
Q99396^.^262^473^.^55074^Alpha46     YDCYEVKTVGDSFMIACKSPFAAVQLAQELQLRFLRLDWGTTVFD 90
HEM_2_0           -      ---*--**--**----------------*--**---*-*---**-
Q99396^.^262^473^.^55074^Alpha91     EFYREFEERHAEEGDGKYKPPTARLDPEVYRQLWNGLRVRVGIHT 135
HEM_2_0           -      -*----------------------------------*--------
Q99396^.^262^473^.^55074^Alpha136    GLCDIRYDEVTKGYDYYGQTANTAARTESVGNGGQVLMTCETYHS 180
HEM_2_0           -      ---------------------------------------------
Q99396^.^262^473^.^55074^Alpha181    LSTAERSQFDVTPLGGVPLRGVSEPVEVYQLN              225
HEM_2_0           -      --------------------------------             
# XX
# > Q99396^.^262^473^.^55074^Alpha^.^0^0^LIGAND^1cs4;^d1cs4a_^FOK^1^1^0^0^1DF^-1000000.00^0.000e+00^0.000e+00
# XX
Q99396^.^262^473^.^55074^Alpha1      KELADPVTLIFTDIESSTAQWATQPELMPDAVATHHSMVRSLIEN 45
FOK_1_0           -      *--------------------------------------------
Q99396^.^262^473^.^55074^Alpha46     YDCYEVKTVGDSFMIACKSPFAAVQLAQELQLRFLRLDWGTTVFD 90
FOK_1_0           -      ---------------------------------------------
Q99396^.^262^473^.^55074^Alpha91     EFYREFEERHAEEGDGKYKPPTARLDPEVYRQLWNGLRVRVGIHT 135
FOK_1_0           -      ---------------------------------------------
Q99396^.^262^473^.^55074^Alpha136    GLCDIRYDEVTKGYDYYGQTANTAARTESVGNGGQVLMTCETYHS 180
FOK_1_0           -      ---------------------------------------------
Q99396^.^262^473^.^55074^Alpha181    LSTAERSQFDVTPLGGVPLRGVSEPVEVYQLN              225
FOK_1_0           -      --------------------------------             

File: aln/Q9DGG6^.^380^560^.^55074^Alpha.aln

# DE   Alignment of query sequence against library of signatures
# XX
# > Q9DGG6^.^380^560^.^55074^Alpha^.^8^52^LIGAND^1cs4;^d1cs4a_^101^1^2^0^0^1DF^5.50^0.000e+00^0.000e+00
# XX
Q9DGG6^.^380^560^.^55074^Alpha1      EQVSILFADIVGFTKMSANKSAHALVGLLNDLFGRFDRLCEDTKC 45
101_1_0           -      --------*---**-------------------------------
Q9DGG6^.^380^560^.^55074^Alpha46     EKISTLGDCYYCVAGCPEPRADHAYCCIEMGLGMIKAIEQFCQEK 90
101_1_0           -      -----***-------------------------------------
Q9DGG6^.^380^560^.^55074^Alpha91     KEMVNMRVGVHTGTVLCGILGMRRFKFDVWSNDVNLANLMEQLGV 135
101_1_0           -      ---------------------------------------------
Q9DGG6^.^380^560^.^55074^Alpha136    AGKVHISEATAKYLDDRYEMEDGKVTERVGQSAVADQLKGLKTYL 180
101_1_0           -      ---------------------------------------------
Q9DGG6^.^380^560^.^55074^Alpha181    I                                             225
101_1_0           -      -                                            
# XX
# > Q9DGG6^.^380^560^.^55074^Alpha^.^8^52^LIGAND^1cs4;^d1cs4a_^MG^1^1^0^0^1DF^5.50^0.000e+00^0.000e+00
# XX
Q9DGG6^.^380^560^.^55074^Alpha1      EQVSILFADIVGFTKMSANKSAHALVGLLNDLFGRFDRLCEDTKC 45
MG_1_0            -      --------**--*--------------------------------
Q9DGG6^.^380^560^.^55074^Alpha46     EKISTLGDCYYCVAGCPEPRADHAYCCIEMGLGMIKAIEQFCQEK 90
MG_1_0            -      -------*-------------------------------------
Q9DGG6^.^380^560^.^55074^Alpha91     KEMVNMRVGVHTGTVLCGILGMRRFKFDVWSNDVNLANLMEQLGV 135
MG_1_0            -      ---------------------------------------------
Q9DGG6^.^380^560^.^55074^Alpha136    AGKVHISEATAKYLDDRYEMEDGKVTERVGQSAVADQLKGLKTYL 180
MG_1_0            -      ---------------------------------------------
Q9DGG6^.^380^560^.^55074^Alpha181    I                                             225
MG_1_0            -      -                                            
# XX
# > Q9DGG6^.^380^560^.^55074^Alpha^.^8^13^LIGAND^1cs4;^d1cs4a_^POP^1^1^0^0^1DF^4.17^0.000e+00^0.000e+00
# XX
Q9DGG6^.^380^560^.^55074^Alpha1      EQVSILFADIVGFTKMSANKSAHALVGLLNDLFGRFDRLCEDTKC 45
POP_1_0           -      --------******-------------------------------
Q9DGG6^.^380^560^.^55074^Alpha46     EKISTLGDCYYCVAGCPEPRADHAYCCIEMGLGMIKAIEQFCQEK 90
POP_1_0           -      ---------------------------------------------
Q9DGG6^.^380^560^.^55074^Alpha91     KEMVNMRVGVHTGTVLCGILGMRRFKFDVWSNDVNLANLMEQLGV 135
POP_1_0           -      ---------------------------------------------
Q9DGG6^.^380^560^.^55074^Alpha136    AGKVHISEATAKYLDDRYEMEDGKVTERVGQSAVADQLKGLKTYL 180
POP_1_0           -      ---------------------------------------------
Q9DGG6^.^380^560^.^55074^Alpha181    I                                             225
POP_1_0           -      -                                            
# XX
# > Q9DGG6^.^380^560^.^55074^Alpha^.^99^179^LIGAND^2hhb;^.^PO4^1^1^0^0^1DF^4.00^0.000e+00^0.000e+00
# XX
Q9DGG6^.^380^560^.^55074^Alpha1      EQVSILFADIVGFTKMSANKSAHALVGLLNDLFGRFDRLCEDTKC 45
PO4_1_0           -      ---------------------------------------------
Q9DGG6^.^380^560^.^55074^Alpha46     EKISTLGDCYYCVAGCPEPRADHAYCCIEMGLGMIKAIEQFCQEK 90
PO4_1_0           -      ---------------------------------------------
Q9DGG6^.^380^560^.^55074^Alpha91     KEMVNMRVGVHTGTVLCGILGMRRFKFDVWSNDVNLANLMEQLGV 135
PO4_1_0           -      ---------*-----------------------------------
Q9DGG6^.^380^560^.^55074^Alpha136    AGKVHISEATAKYLDDRYEMEDGKVTERVGQSAVADQLKGLKTYL 180


  [Part of this file has been deleted for brevity]

# > Q9DGG6^.^380^560^.^55074^Alpha^.^84^178^LIGAND^2hhb;^.^HEM^1^4^0^0^1DF^0.82^0.000e+00^0.000e+00
# XX
Q9DGG6^.^380^560^.^55074^Alpha1      EQVSILFADIVGFTKMSANKSAHALVGLLNDLFGRFDRLCEDTKC 45
HEM_1_0           -      ---------------------------------------------
Q9DGG6^.^380^560^.^55074^Alpha46     EKISTLGDCYYCVAGCPEPRADHAYCCIEMGLGMIKAIEQFCQEK 90
HEM_1_0           -      ---------------------------------------**-**-
Q9DGG6^.^380^560^.^55074^Alpha91     KEMVNMRVGVHTGTVLCGILGMRRFKFDVWSNDVNLANLMEQLGV 135
HEM_1_0           -      ----------*--**--*-----------------*--**---*-
Q9DGG6^.^380^560^.^55074^Alpha136    AGKVHISEATAKYLDDRYEMEDGKVTERVGQSAVADQLKGLKTYL 180
HEM_1_0           -      *---**--*----------------------------------*-
Q9DGG6^.^380^560^.^55074^Alpha181    I                                             225
HEM_1_0           -      -                                            
# XX
# > Q9DGG6^.^380^560^.^55074^Alpha^.^68^178^LIGAND^2hhb;^.^HEM^2^4^0^0^1DF^0.65^0.000e+00^0.000e+00
# XX
Q9DGG6^.^380^560^.^55074^Alpha1      EQVSILFADIVGFTKMSANKSAHALVGLLNDLFGRFDRLCEDTKC 45
HEM_2_0           -      ---------------------------------------------
Q9DGG6^.^380^560^.^55074^Alpha46     EKISTLGDCYYCVAGCPEPRADHAYCCIEMGLGMIKAIEQFCQEK 90
HEM_2_0           -      -----------------------*---------**----------
Q9DGG6^.^380^560^.^55074^Alpha91     KEMVNMRVGVHTGTVLCGILGMRRFKFDVWSNDVNLANLMEQLGV 135
HEM_2_0           -      ----------*--**--**----------------*--**---*-
Q9DGG6^.^380^560^.^55074^Alpha136    AGKVHISEATAKYLDDRYEMEDGKVTERVGQSAVADQLKGLKTYL 180
HEM_2_0           -      *---**--*----------------------------------*-
Q9DGG6^.^380^560^.^55074^Alpha181    I                                             225
HEM_2_0           -      -                                            
# XX
# > Q9DGG6^.^380^560^.^55074^Alpha^.^68^178^LIGAND^2hhb;^.^HEM^4^4^0^0^1DF^0.47^0.000e+00^0.000e+00
# XX
Q9DGG6^.^380^560^.^55074^Alpha1      EQVSILFADIVGFTKMSANKSAHALVGLLNDLFGRFDRLCEDTKC 45
HEM_4_0           -      ---------------------------------------------
Q9DGG6^.^380^560^.^55074^Alpha46     EKISTLGDCYYCVAGCPEPRADHAYCCIEMGLGMIKAIEQFCQEK 90
HEM_4_0           -      -----------------------*---------**----------
Q9DGG6^.^380^560^.^55074^Alpha91     KEMVNMRVGVHTGTVLCGILGMRRFKFDVWSNDVNLANLMEQLGV 135
HEM_4_0           -      ----------*--**--*--------------------**---*-
Q9DGG6^.^380^560^.^55074^Alpha136    AGKVHISEATAKYLDDRYEMEDGKVTERVGQSAVADQLKGLKTYL 180
HEM_4_0           -      *---**--*----------------------------------*-
Q9DGG6^.^380^560^.^55074^Alpha181    I                                             225
HEM_4_0           -      -                                            
# XX
# > Q9DGG6^.^380^560^.^55074^Alpha^.^0^0^LIGAND^1cs4;^d1cs4a_^FOK^1^1^0^0^1DF^-1000000.00^0.000e+00^0.000e+00
# XX
Q9DGG6^.^380^560^.^55074^Alpha1      EQVSILFADIVGFTKMSANKSAHALVGLLNDLFGRFDRLCEDTKC 45
FOK_1_0           -      *--------------------------------------------
Q9DGG6^.^380^560^.^55074^Alpha46     EKISTLGDCYYCVAGCPEPRADHAYCCIEMGLGMIKAIEQFCQEK 90
FOK_1_0           -      ---------------------------------------------
Q9DGG6^.^380^560^.^55074^Alpha91     KEMVNMRVGVHTGTVLCGILGMRRFKFDVWSNDVNLANLMEQLGV 135
FOK_1_0           -      ---------------------------------------------
Q9DGG6^.^380^560^.^55074^Alpha136    AGKVHISEATAKYLDDRYEMEDGKVTERVGQSAVADQLKGLKTYL 180
FOK_1_0           -      ---------------------------------------------
Q9DGG6^.^380^560^.^55074^Alpha181    I                                             225
FOK_1_0           -      -                                            

File: aln/Q9ERL9^.^480^631^.^55074^Alpha.aln

# DE   Alignment of query sequence against library of signatures
# XX
# > Q9ERL9^.^480^631^.^55074^Alpha^.^6^50^LIGAND^1cs4;^d1cs4a_^MG^1^1^0^0^1DF^5.50^0.000e+00^0.000e+00
# XX
Q9ERL9^.^480^631^.^55074^Alpha1      VTMLFSDIVGFTAICSQCSPLQVITMLNALYTRFDQQCGELDVYK 45
MG_1_0            -      ------**--*----------------------------------
Q9ERL9^.^480^631^.^55074^Alpha46     VETIGDAYCVAGGLHRESDTHAVQIALMALKMMELSNEVMSPHGE 90
MG_1_0            -      -----*---------------------------------------
Q9ERL9^.^480^631^.^55074^Alpha91     PIKMRIGLHSGSVFAGVVGVKMPRYCLFGNNVTLANKFESCSVPR 135
MG_1_0            -      ---------------------------------------------
Q9ERL9^.^480^631^.^55074^Alpha136    KINVSPTTYRLLKDCPG                             180
MG_1_0            -      -----------------                            
# XX
# > Q9ERL9^.^480^631^.^55074^Alpha^.^6^50^LIGAND^1cs4;^d1cs4a_^101^1^2^0^0^1DF^5.17^0.000e+00^0.000e+00
# XX
Q9ERL9^.^480^631^.^55074^Alpha1      VTMLFSDIVGFTAICSQCSPLQVITMLNALYTRFDQQCGELDVYK 45
101_1_0           -      ------*---**---------------------------------
Q9ERL9^.^480^631^.^55074^Alpha46     VETIGDAYCVAGGLHRESDTHAVQIALMALKMMELSNEVMSPHGE 90
101_1_0           -      ---***---------------------------------------
Q9ERL9^.^480^631^.^55074^Alpha91     PIKMRIGLHSGSVFAGVVGVKMPRYCLFGNNVTLANKFESCSVPR 135
101_1_0           -      ---------------------------------------------
Q9ERL9^.^480^631^.^55074^Alpha136    KINVSPTTYRLLKDCPG                             180
101_1_0           -      -----------------                            
# XX
# > Q9ERL9^.^480^631^.^55074^Alpha^.^98^137^LIGAND^1ii7;^d1ii7a_^101^2^2^0^0^1DF^4.50^0.000e+00^0.000e+00
# XX
Q9ERL9^.^480^631^.^55074^Alpha1      VTMLFSDIVGFTAICSQCSPLQVITMLNALYTRFDQQCGELDVYK 45
101_2_0           -      ---------------------------------------------
Q9ERL9^.^480^631^.^55074^Alpha46     VETIGDAYCVAGGLHRESDTHAVQIALMALKMMELSNEVMSPHGE 90
101_2_0           -      ---------------------------------------------
Q9ERL9^.^480^631^.^55074^Alpha91     PIKMRIGLHSGSVFAGVVGVKMPRYCLFGNNVTLANKFESCSVPR 135
101_2_0           -      --------*------------------------------------
Q9ERL9^.^480^631^.^55074^Alpha136    KINVSPTTYRLLKDCPG                             180
101_2_0           -      --*--------------                            
# XX
# > Q9ERL9^.^480^631^.^55074^Alpha^.^6^11^LIGAND^1cs4;^d1cs4a_^POP^1^1^0^0^1DF^4.17^0.000e+00^0.000e+00
# XX
Q9ERL9^.^480^631^.^55074^Alpha1      VTMLFSDIVGFTAICSQCSPLQVITMLNALYTRFDQQCGELDVYK 45
POP_1_0           -      ------******---------------------------------
Q9ERL9^.^480^631^.^55074^Alpha46     VETIGDAYCVAGGLHRESDTHAVQIALMALKMMELSNEVMSPHGE 90
POP_1_0           -      ---------------------------------------------
Q9ERL9^.^480^631^.^55074^Alpha91     PIKMRIGLHSGSVFAGVVGVKMPRYCLFGNNVTLANKFESCSVPR 135
POP_1_0           -      ---------------------------------------------
Q9ERL9^.^480^631^.^55074^Alpha136    KINVSPTTYRLLKDCPG                             180
POP_1_0           -      -----------------                            
# XX
# > Q9ERL9^.^480^631^.^55074^Alpha^.^63^104^LIGAND^1ii7;^d1ii7a_^MN^1^1^0^0^1DF^4.00^0.000e+00^0.000e+00
# XX
Q9ERL9^.^480^631^.^55074^Alpha1      VTMLFSDIVGFTAICSQCSPLQVITMLNALYTRFDQQCGELDVYK 45
MN_1_0            -      ---------------------------------------------


  [Part of this file has been deleted for brevity]

HEM_4_0           -      ----*---------**--------------------*--**--*-
Q9ERL9^.^480^631^.^55074^Alpha46     VETIGDAYCVAGGLHRESDTHAVQIALMALKMMELSNEVMSPHGE 90
HEM_4_0           -      -------------------**---*-*---**--*----------
Q9ERL9^.^480^631^.^55074^Alpha91     PIKMRIGLHSGSVFAGVVGVKMPRYCLFGNNVTLANKFESCSVPR 135
HEM_4_0           -      ------------------------*--------------------
Q9ERL9^.^480^631^.^55074^Alpha136    KINVSPTTYRLLKDCPG                             180
HEM_4_0           -      -----------------                            
# XX
# > Q9ERL9^.^480^631^.^55074^Alpha^.^25^119^LIGAND^2hhb;^.^HEM^1^4^0^0^1DF^0.29^0.000e+00^0.000e+00
# XX
Q9ERL9^.^480^631^.^55074^Alpha1      VTMLFSDIVGFTAICSQCSPLQVITMLNALYTRFDQQCGELDVYK 45
HEM_1_0           -      -------------------------**-**-----------*--*
Q9ERL9^.^480^631^.^55074^Alpha46     VETIGDAYCVAGGLHRESDTHAVQIALMALKMMELSNEVMSPHGE 90
HEM_1_0           -      *--*-----------------*--**---*-*---**--*-----
Q9ERL9^.^480^631^.^55074^Alpha91     PIKMRIGLHSGSVFAGVVGVKMPRYCLFGNNVTLANKFESCSVPR 135
HEM_1_0           -      -----------------------------*---------------
Q9ERL9^.^480^631^.^55074^Alpha136    KINVSPTTYRLLKDCPG                             180
HEM_1_0           -      -----------------                            
# XX
# > Q9ERL9^.^480^631^.^55074^Alpha^.^12^122^LIGAND^2hhb;^.^HEM^2^4^0^0^1DF^0.24^0.000e+00^0.000e+00
# XX
Q9ERL9^.^480^631^.^55074^Alpha1      VTMLFSDIVGFTAICSQCSPLQVITMLNALYTRFDQQCGELDVYK 45
HEM_2_0           -      ------------*---------**--------------------*
Q9ERL9^.^480^631^.^55074^Alpha46     VETIGDAYCVAGGLHRESDTHAVQIALMALKMMELSNEVMSPHGE 90
HEM_2_0           -      --**--**----------------*--**---*-*---**--*--
Q9ERL9^.^480^631^.^55074^Alpha91     PIKMRIGLHSGSVFAGVVGVKMPRYCLFGNNVTLANKFESCSVPR 135
HEM_2_0           -      --------------------------------*------------
Q9ERL9^.^480^631^.^55074^Alpha136    KINVSPTTYRLLKDCPG                             180
HEM_2_0           -      -----------------                            
# XX
# > Q9ERL9^.^480^631^.^55074^Alpha^.^15^119^LIGAND^2hhb;^.^HEM^3^4^0^0^1DF^0.21^0.000e+00^0.000e+00
# XX
Q9ERL9^.^480^631^.^55074^Alpha1      VTMLFSDIVGFTAICSQCSPLQVITMLNALYTRFDQQCGELDVYK 45
HEM_3_0           -      ---------------*------*--**-**-----------*--*
Q9ERL9^.^480^631^.^55074^Alpha46     VETIGDAYCVAGGLHRESDTHAVQIALMALKMMELSNEVMSPHGE 90
HEM_3_0           -      *--*-----------------*--**---*-*---**--*-----
Q9ERL9^.^480^631^.^55074^Alpha91     PIKMRIGLHSGSVFAGVVGVKMPRYCLFGNNVTLANKFESCSVPR 135
HEM_3_0           -      -----------------------------*---------------
Q9ERL9^.^480^631^.^55074^Alpha136    KINVSPTTYRLLKDCPG                             180
HEM_3_0           -      -----------------                            
# XX
# > Q9ERL9^.^480^631^.^55074^Alpha^.^0^0^LIGAND^1cs4;^d1cs4a_^FOK^1^1^0^0^1DF^-1000000.00^0.000e+00^0.000e+00
# XX
Q9ERL9^.^480^631^.^55074^Alpha1      VTMLFSDIVGFTAICSQCSPLQVITMLNALYTRFDQQCGELDVYK 45
FOK_1_0           -      *--------------------------------------------
Q9ERL9^.^480^631^.^55074^Alpha46     VETIGDAYCVAGGLHRESDTHAVQIALMALKMMELSNEVMSPHGE 90
FOK_1_0           -      ---------------------------------------------
Q9ERL9^.^480^631^.^55074^Alpha91     PIKMRIGLHSGSVFAGVVGVKMPRYCLFGNNVTLANKFESCSVPR 135
FOK_1_0           -      ---------------------------------------------
Q9ERL9^.^480^631^.^55074^Alpha136    KINVSPTTYRLLKDCPG                             180
FOK_1_0           -      -----------------                            

File: aln/Q9WVI4^.^516^664^.^55074^Alpha.aln

# DE   Alignment of query sequence against library of signatures
# XX
# > Q9WVI4^.^516^664^.^55074^Alpha^.^8^52^LIGAND^1cs4;^d1cs4a_^MG^1^1^0^0^1DF^5.50^0.000e+00^0.000e+00
# XX
Q9WVI4^.^516^664^.^55074^Alpha1      DDVTMLFSDIVGFTAICAQCTPMQVISMLNELYTRFDHQCGFLDI 45
MG_1_0            -      --------**--*--------------------------------
Q9WVI4^.^516^664^.^55074^Alpha46     YKVETIGDAYCVASGLHRKSLCHAKPIALMALKMMELSEEVLTPD 90
MG_1_0            -      -------*-------------------------------------
Q9WVI4^.^516^664^.^55074^Alpha91     GRPIQMRIGIHSGSVLAGVVGVRMPRYCLFGNNVTLASKFESGSH 135
MG_1_0            -      ---------------------------------------------
Q9WVI4^.^516^664^.^55074^Alpha136    PRRINISPTTYQLL                                180
MG_1_0            -      --------------                               
# XX
# > Q9WVI4^.^516^664^.^55074^Alpha^.^8^52^LIGAND^1cs4;^d1cs4a_^101^1^2^0^0^1DF^5.17^0.000e+00^0.000e+00
# XX
Q9WVI4^.^516^664^.^55074^Alpha1      DDVTMLFSDIVGFTAICAQCTPMQVISMLNELYTRFDHQCGFLDI 45
101_1_0           -      --------*---**-------------------------------
Q9WVI4^.^516^664^.^55074^Alpha46     YKVETIGDAYCVASGLHRKSLCHAKPIALMALKMMELSEEVLTPD 90
101_1_0           -      -----***-------------------------------------
Q9WVI4^.^516^664^.^55074^Alpha91     GRPIQMRIGIHSGSVLAGVVGVRMPRYCLFGNNVTLASKFESGSH 135
101_1_0           -      ---------------------------------------------
Q9WVI4^.^516^664^.^55074^Alpha136    PRRINISPTTYQLL                                180
101_1_0           -      --------------                               
# XX
# > Q9WVI4^.^516^664^.^55074^Alpha^.^100^139^LIGAND^1ii7;^d1ii7a_^101^2^2^0^0^1DF^4.50^0.000e+00^0.000e+00
# XX
Q9WVI4^.^516^664^.^55074^Alpha1      DDVTMLFSDIVGFTAICAQCTPMQVISMLNELYTRFDHQCGFLDI 45
101_2_0           -      ---------------------------------------------
Q9WVI4^.^516^664^.^55074^Alpha46     YKVETIGDAYCVASGLHRKSLCHAKPIALMALKMMELSEEVLTPD 90
101_2_0           -      ---------------------------------------------
Q9WVI4^.^516^664^.^55074^Alpha91     GRPIQMRIGIHSGSVLAGVVGVRMPRYCLFGNNVTLASKFESGSH 135
101_2_0           -      ----------*----------------------------------
Q9WVI4^.^516^664^.^55074^Alpha136    PRRINISPTTYQLL                                180
101_2_0           -      ----*---------                               
# XX
# > Q9WVI4^.^516^664^.^55074^Alpha^.^8^13^LIGAND^1cs4;^d1cs4a_^POP^1^1^0^0^1DF^4.17^0.000e+00^0.000e+00
# XX
Q9WVI4^.^516^664^.^55074^Alpha1      DDVTMLFSDIVGFTAICAQCTPMQVISMLNELYTRFDHQCGFLDI 45
POP_1_0           -      --------******-------------------------------
Q9WVI4^.^516^664^.^55074^Alpha46     YKVETIGDAYCVASGLHRKSLCHAKPIALMALKMMELSEEVLTPD 90
POP_1_0           -      ---------------------------------------------
Q9WVI4^.^516^664^.^55074^Alpha91     GRPIQMRIGIHSGSVLAGVVGVRMPRYCLFGNNVTLASKFESGSH 135
POP_1_0           -      ---------------------------------------------
Q9WVI4^.^516^664^.^55074^Alpha136    PRRINISPTTYQLL                                180
POP_1_0           -      --------------                               
# XX
# > Q9WVI4^.^516^664^.^55074^Alpha^.^25^105^LIGAND^2hhb;^.^PO4^1^1^0^0^1DF^3.50^0.000e+00^0.000e+00
# XX
Q9WVI4^.^516^664^.^55074^Alpha1      DDVTMLFSDIVGFTAICAQCTPMQVISMLNELYTRFDHQCGFLDI 45
PO4_1_0           -      -------------------------*-------------------


  [Part of this file has been deleted for brevity]

HEM_1_0           -      ---------------------------**-**-----------*-
Q9WVI4^.^516^664^.^55074^Alpha46     YKVETIGDAYCVASGLHRKSLCHAKPIALMALKMMELSEEVLTPD 90
HEM_1_0           -      -**--*-----------------*--**---*-*---**--*---
Q9WVI4^.^516^664^.^55074^Alpha91     GRPIQMRIGIHSGSVLAGVVGVRMPRYCLFGNNVTLASKFESGSH 135
HEM_1_0           -      -------------------------------*-------------
Q9WVI4^.^516^664^.^55074^Alpha136    PRRINISPTTYQLL                                180
HEM_1_0           -      --------------                               
# XX
# > Q9WVI4^.^516^664^.^55074^Alpha^.^17^121^LIGAND^2hhb;^.^HEM^3^4^0^0^1DF^0.42^0.000e+00^0.000e+00
# XX
Q9WVI4^.^516^664^.^55074^Alpha1      DDVTMLFSDIVGFTAICAQCTPMQVISMLNELYTRFDHQCGFLDI 45
HEM_3_0           -      -----------------*------*--**-**-----------*-
Q9WVI4^.^516^664^.^55074^Alpha46     YKVETIGDAYCVASGLHRKSLCHAKPIALMALKMMELSEEVLTPD 90
HEM_3_0           -      -**--*-----------------*--**---*-*---**--*---
Q9WVI4^.^516^664^.^55074^Alpha91     GRPIQMRIGIHSGSVLAGVVGVRMPRYCLFGNNVTLASKFESGSH 135
HEM_3_0           -      -------------------------------*-------------
Q9WVI4^.^516^664^.^55074^Alpha136    PRRINISPTTYQLL                                180
HEM_3_0           -      --------------                               
# XX
# > Q9WVI4^.^516^664^.^55074^Alpha^.^6^116^LIGAND^2hhb;^.^HEM^4^4^0^0^1DF^0.33^0.000e+00^0.000e+00
# XX
Q9WVI4^.^516^664^.^55074^Alpha1      DDVTMLFSDIVGFTAICAQCTPMQVISMLNELYTRFDHQCGFLDI 45
HEM_4_0           -      ------*---------**--------------------*--**--
Q9WVI4^.^516^664^.^55074^Alpha46     YKVETIGDAYCVASGLHRKSLCHAKPIALMALKMMELSEEVLTPD 90
HEM_4_0           -      *--------------------**---*-*---**--*--------
Q9WVI4^.^516^664^.^55074^Alpha91     GRPIQMRIGIHSGSVLAGVVGVRMPRYCLFGNNVTLASKFESGSH 135
HEM_4_0           -      --------------------------*------------------
Q9WVI4^.^516^664^.^55074^Alpha136    PRRINISPTTYQLL                                180
HEM_4_0           -      --------------                               
# XX
# > Q9WVI4^.^516^664^.^55074^Alpha^.^14^124^LIGAND^2hhb;^.^HEM^2^4^0^0^1DF^0.18^0.000e+00^0.000e+00
# XX
Q9WVI4^.^516^664^.^55074^Alpha1      DDVTMLFSDIVGFTAICAQCTPMQVISMLNELYTRFDHQCGFLDI 45
HEM_2_0           -      --------------*---------**-------------------
Q9WVI4^.^516^664^.^55074^Alpha46     YKVETIGDAYCVASGLHRKSLCHAKPIALMALKMMELSEEVLTPD 90
HEM_2_0           -      -*--**--**----------------*--**---*-*---**--*
Q9WVI4^.^516^664^.^55074^Alpha91     GRPIQMRIGIHSGSVLAGVVGVRMPRYCLFGNNVTLASKFESGSH 135
HEM_2_0           -      ----------------------------------*----------
Q9WVI4^.^516^664^.^55074^Alpha136    PRRINISPTTYQLL                                180
HEM_2_0           -      --------------                               
# XX
# > Q9WVI4^.^516^664^.^55074^Alpha^.^0^0^LIGAND^1cs4;^d1cs4a_^FOK^1^1^0^0^1DF^-1000000.00^0.000e+00^0.000e+00
# XX
Q9WVI4^.^516^664^.^55074^Alpha1      DDVTMLFSDIVGFTAICAQCTPMQVISMLNELYTRFDHQCGFLDI 45
FOK_1_0           -      *--------------------------------------------
Q9WVI4^.^516^664^.^55074^Alpha46     YKVETIGDAYCVASGLHRKSLCHAKPIALMALKMMELSEEVLTPD 90
FOK_1_0           -      ---------------------------------------------
Q9WVI4^.^516^664^.^55074^Alpha91     GRPIQMRIGIHSGSVLAGVVGVRMPRYCLFGNNVTLASKFESGSH 135
FOK_1_0           -      ---------------------------------------------
Q9WVI4^.^516^664^.^55074^Alpha136    PRRINISPTTYQLL                                180
FOK_1_0           -      --------------                               

Directory: results

This directory contains output files, for example Q99396^.^262^473^.^55074^Alpha.results Q9DGG6^.^380^560^.^55074^Alpha.results Q9ERL9^.^480^631^.^55074^Alpha.results and Q9WVI4^.^516^664^.^55074^Alpha.results.

File: results/Q99396^.^262^473^.^55074^Alpha.results

LIGID     PATCHES   SITES     SCORE     
MN        1         1         5.33      
101       2         2         4.42      
PO4       1         1         4.00      
POP       1         1         3.00      
MG        1         1         2.00      
HEM       4         4         0.82      
FOK       1         1         -1000000.00

File: results/Q9DGG6^.^380^560^.^55074^Alpha.results

LIGID     PATCHES   SITES     SCORE     
MG        1         1         5.50      
101       2         2         4.50      
POP       1         1         4.17      
PO4       1         1         4.00      
MN        1         1         2.33      
HEM       4         4         0.73      
FOK       1         1         -1000000.00

File: results/Q9ERL9^.^480^631^.^55074^Alpha.results

LIGID     PATCHES   SITES     SCORE     
MG        1         1         5.50      
101       2         2         4.83      
POP       1         1         4.17      
MN        1         1         4.00      
PO4       1         1         2.50      
HEM       4         4         0.33      
FOK       1         1         -1000000.00

File: results/Q9WVI4^.^516^664^.^55074^Alpha.results

LIGID     PATCHES   SITES     SCORE     
MG        1         1         5.50      
101       2         2         4.83      
POP       1         1         4.17      
PO4       1         1         3.50      
MN        1         1         3.33      
HEM       4         4         0.37      
FOK       1         1         -1000000.00




5.0 DATA FILES

SIGSCANLIG requires a matrix of 3D:1D scores (residue:environment scoring matrix).


6.0 USAGE

Searches ligand-signature library and writes hits (LHF file)
Version: EMBOSS:6.4.0.0

   Standard (Mandatory) qualifiers:
  [-siginfilesdir]     dirlist    [./] This option specifies the directory of
                                  signature files (input). A 'signature file'
                                  contains a sparse sequence signature
                                  suitable for use with the SIGSCAN and
                                  SIGSCANLIG programs. The files are generated
                                  by using SIGGEN and SIGGENLIG.
  [-dbseqall]          seqall     This option specifies the name of the
                                  database of query sequences.
   -sub                matrixf    [EBLOSUM62] This option specifies the
                                  scoring matrix to use, e.g. residue
                                  substitution matrix (1D signatures) or
                                  matrix of 3D:1D (environment:residue) scores
                                  (3D).
   -mode               menu       [1] This option specifies the mode of
                                  scoring ligands. In 'Patch Score Mode' (mode
                                  1) the score for a ligand is the mean of
                                  its patch scores. In 'Site Score Mode' the
                                  score for a ligand is the mean of its site
                                  scores. A site score is the mean of patch
                                  score for all patches for a given site.
                                  (Values: 1 (Patch score mode); 2 (Site score
                                  mode))
   -gapo               float      [10.0 for any sequence] This option
                                  specifies the gap insertion penalty. The gap
                                  insertion penalty is the score taken away
                                  when a gap is created. The best value
                                  depends on the choice of comparison matrix.
                                  The default value assumes you are using the
                                  EBLOSUM62 matrix for protein sequences, and
                                  the EDNAMAT matrix for nucleotide sequences.
                                  (Floating point number from 1.0 to 100.0)
   -gape               float      [0.5 for any sequence] This option specifies
                                  the gap extension penalty. The gap
                                  extension penalty is added to the standard
                                  gap penalty for each base or residue in the
                                  gap. This is how long gaps are penalized.
                                  Usually you will expect a few long gaps
                                  rather than many short gaps, so the gap
                                  extension penalty should be lower than the
                                  gap penalty. (Floating point number from 0.0
                                  to 10.0)
   -nterm              menu       [1] This option specifies the N-terminal
                                  matching option. This determines how the
                                  first signature position is aligned to a
                                  sequence from the database. (Values: 1
                                  (Align anywhere and allow only complete
                                  signature-sequence fit); 2 (Align anywhere
                                  and allow partial signature-sequence fit); 3
                                  (Use empirical gaps only))
  [-hitsoutdir]        outdir     [./] This option specifies the directory of
                                  the LHF files (ligand hits files) (output).
                                  A 'ligand hits file' contains database hits
                                  (sequences) with ligand classification
                                  information, in the LHF format (FASTA-like).
                                  The hits are putative ligand-binding
                                  sequences and are found from a search of a
                                  sequence database, in this case, by using
                                  SIGSCANLIG.
  [-alignoutdir]       outdir     [./] This option specifies the name of the
                                  SAF (signature alignment file) (output).A
                                  'signature alignment file' contains one or
                                  more signnature-sequence alignments. The
                                  file is in DAF format (CLUSTAL-like) and is
                                  annotated with bibliographic information,
                                  either the domain family classification (for
                                  SIGSCAN output) or ligand classification
                                  (for SIGSCANLIG output). The files generated
                                  by SIGSCAN will contain a
                                  signature-sequence alignment for a single
                                  signature against a library of one or more
                                  sequences. The files generated by using
                                  SIGSCANLIG will contain a signature-sequence
                                  alignment for a single query sequence
                                  against a library of one or more signatures.
  [-resultsoutdir]     outdir     [./] This option specifies the directory for
                                  the results files. A results file is
                                  generated for each query sequence and
                                  contains a list of hits (ligands),
                                  rank-ordered on the basis of score.

   Additional (Optional) qualifiers (* if not always prompted):
   -nhits              integer    [100] This option specifies the maximum
                                  number of hits to output. (Any integer
                                  value)
   -domax              toggle     [N] This option specifies whether to
                                  consider a max. number of top-scoring hits
                                  only for each ligand.
*  -maxhits            integer    [0] This option specifies the maximum number
                                  of top-scoring hits to consider for each
                                  ligand. (Any integer value)

   Advanced (Unprompted) qualifiers: (none)
   Associated qualifiers:

   "-siginfilesdir" associated qualifiers
   -extension1         string     Default file extension

   "-dbseqall" associated qualifiers
   -sbegin2            integer    Start of each sequence to be used
   -send2              integer    End of each sequence to be used
   -sreverse2          boolean    Reverse (if DNA)
   -sask2              boolean    Ask for begin/end/reverse
   -snucleotide2       boolean    Sequence is nucleotide
   -sprotein2          boolean    Sequence is protein
   -slower2            boolean    Make lower case
   -supper2            boolean    Make upper case
   -sformat2           string     Input sequence format
   -sdbname2           string     Database name
   -sid2               string     Entryname
   -ufo2               string     UFO features
   -fformat2           string     Features format
   -fopenfile2         string     Features file name

   "-hitsoutdir" associated qualifiers
   -extension3         string     Default file extension

   "-alignoutdir" associated qualifiers
   -extension4         string     Default file extension

   "-resultsoutdir" associated qualifiers
   -extension5         string     Default file extension

   General qualifiers:
   -auto               boolean    Turn off prompts
   -stdout             boolean    Write first file to standard output
   -filter             boolean    Read first file from standard input, write
                                  first file to standard output
   -options            boolean    Prompt for standard and additional values
   -debug              boolean    Write debug output to program.dbg
   -verbose            boolean    Report some/full command line options
   -help               boolean    Report command line options and exit. More
                                  information on associated and general
                                  qualifiers can be found with -help -verbose
   -warning            boolean    Report warnings
   -error              boolean    Report errors
   -fatal              boolean    Report fatal errors
   -die                boolean    Report dying program messages
   -version            boolean    Report version number and exit

6.1 COMMAND LINE ARGUMENTS

Qualifier Type Description Allowed values Default
Standard (Mandatory) qualifiers
[-siginfilesdir]
(Parameter 1)
dirlist This option specifies the directory of signature files (input). A 'signature file' contains a sparse sequence signature suitable for use with the SIGSCAN and SIGSCANLIG programs. The files are generated by using SIGGEN and SIGGENLIG. Directory with files ./
[-dbseqall]
(Parameter 2)
seqall This option specifies the name of the database of query sequences. Readable sequence(s) Required
-sub matrixf This option specifies the scoring matrix to use, e.g. residue substitution matrix (1D signatures) or matrix of 3D:1D (environment:residue) scores (3D). Comparison matrix file in EMBOSS data path EBLOSUM62
-mode list This option specifies the mode of scoring ligands. In 'Patch Score Mode' (mode 1) the score for a ligand is the mean of its patch scores. In 'Site Score Mode' the score for a ligand is the mean of its site scores. A site score is the mean of patch score for all patches for a given site.
1 (Patch score mode)
2 (Site score mode)
1
-gapo float This option specifies the gap insertion penalty. The gap insertion penalty is the score taken away when a gap is created. The best value depends on the choice of comparison matrix. The default value assumes you are using the EBLOSUM62 matrix for protein sequences, and the EDNAMAT matrix for nucleotide sequences. Floating point number from 1.0 to 100.0 10.0 for any sequence
-gape float This option specifies the gap extension penalty. The gap extension penalty is added to the standard gap penalty for each base or residue in the gap. This is how long gaps are penalized. Usually you will expect a few long gaps rather than many short gaps, so the gap extension penalty should be lower than the gap penalty. Floating point number from 0.0 to 10.0 0.5 for any sequence
-nterm list This option specifies the N-terminal matching option. This determines how the first signature position is aligned to a sequence from the database.
1 (Align anywhere and allow only complete signature-sequence fit)
2 (Align anywhere and allow partial signature-sequence fit)
3 (Use empirical gaps only)
1
[-hitsoutdir]
(Parameter 3)
outdir This option specifies the directory of the LHF files (ligand hits files) (output). A 'ligand hits file' contains database hits (sequences) with ligand classification information, in the LHF format (FASTA-like). The hits are putative ligand-binding sequences and are found from a search of a sequence database, in this case, by using SIGSCANLIG. Output directory ./
[-alignoutdir]
(Parameter 4)
outdir This option specifies the name of the SAF (signature alignment file) (output).A 'signature alignment file' contains one or more signnature-sequence alignments. The file is in DAF format (CLUSTAL-like) and is annotated with bibliographic information, either the domain family classification (for SIGSCAN output) or ligand classification (for SIGSCANLIG output). The files generated by SIGSCAN will contain a signature-sequence alignment for a single signature against a library of one or more sequences. The files generated by using SIGSCANLIG will contain a signature-sequence alignment for a single query sequence against a library of one or more signatures. Output directory ./
[-resultsoutdir]
(Parameter 5)
outdir This option specifies the directory for the results files. A results file is generated for each query sequence and contains a list of hits (ligands), rank-ordered on the basis of score. Output directory ./
Additional (Optional) qualifiers
-nhits integer This option specifies the maximum number of hits to output. Any integer value 100
-domax toggle This option specifies whether to consider a max. number of top-scoring hits only for each ligand. Toggle value Yes/No No
-maxhits integer This option specifies the maximum number of top-scoring hits to consider for each ligand. Any integer value 0
Advanced (Unprompted) qualifiers
(none)
Associated qualifiers
"-siginfilesdir" associated dirlist qualifiers
-extension1
-extension_siginfilesdir
string Default file extension Any string sig
"-dbseqall" associated seqall qualifiers
-sbegin2
-sbegin_dbseqall
integer Start of each sequence to be used Any integer value 0
-send2
-send_dbseqall
integer End of each sequence to be used Any integer value 0
-sreverse2
-sreverse_dbseqall
boolean Reverse (if DNA) Boolean value Yes/No N
-sask2
-sask_dbseqall
boolean Ask for begin/end/reverse Boolean value Yes/No N
-snucleotide2
-snucleotide_dbseqall
boolean Sequence is nucleotide Boolean value Yes/No N
-sprotein2
-sprotein_dbseqall
boolean Sequence is protein Boolean value Yes/No N
-slower2
-slower_dbseqall
boolean Make lower case Boolean value Yes/No N
-supper2
-supper_dbseqall
boolean Make upper case Boolean value Yes/No N
-sformat2
-sformat_dbseqall
string Input sequence format Any string  
-sdbname2
-sdbname_dbseqall
string Database name Any string  
-sid2
-sid_dbseqall
string Entryname Any string  
-ufo2
-ufo_dbseqall
string UFO features Any string  
-fformat2
-fformat_dbseqall
string Features format Any string  
-fopenfile2
-fopenfile_dbseqall
string Features file name Any string  
"-hitsoutdir" associated outdir qualifiers
-extension3
-extension_hitsoutdir
string Default file extension Any string lhf
"-alignoutdir" associated outdir qualifiers
-extension4
-extension_alignoutdir
string Default file extension Any string aln
"-resultsoutdir" associated outdir qualifiers
-extension5
-extension_resultsoutdir
string Default file extension Any string results
General qualifiers
-auto boolean Turn off prompts Boolean value Yes/No N
-stdout boolean Write first file to standard output Boolean value Yes/No N
-filter boolean Read first file from standard input, write first file to standard output Boolean value Yes/No N
-options boolean Prompt for standard and additional values Boolean value Yes/No N
-debug boolean Write debug output to program.dbg Boolean value Yes/No N
-verbose boolean Report some/full command line options Boolean value Yes/No Y
-help boolean Report command line options and exit. More information on associated and general qualifiers can be found with -help -verbose Boolean value Yes/No N
-warning boolean Report warnings Boolean value Yes/No Y
-error boolean Report errors Boolean value Yes/No Y
-fatal boolean Report fatal errors Boolean value Yes/No Y
-die boolean Report dying program messages Boolean value Yes/No Y
-version boolean Report version number and exit Boolean value Yes/No N

6.2 EXAMPLE SESSION

An example of interactive use of SIGSCANLIG is shown below. Here is a sample session with sigscanlig


% sigscanlig 
Searches ligand-signature library and writes hits (LHF file)
Domainatrix signature directories [./]: ../siggenlig-keep
Database of query sequences.: swtiny
Scoring matrix [EBLOSUM62]: 
Available modes
         1 : Patch score mode
         2 : Site score mode
Select mode of scoring ligands. [1]: 1
Gap insertion penalty [10]: 
Gap extension penalty [0.5]: 
N-terminal matching options
         1 : Align anywhere and allow only complete signature-sequence fit
         2 : Align anywhere and allow partial signature-sequence fit
         3 : Use empirical gaps only
Select number [1]: 
Domainatrix LHF ligand hits file output directory [./]: lhf
Domainatrix signature alignment file output directory [./]: aln
Domainatrix sigscanlig program output file output directory [./]: results

Go to the input files for this example
Go to the output files for this example




7.0 KNOWN BUGS & WARNINGS

None.


8.0 NOTES

SIGSCANLIG does not generate p-values or E-values and a value of '0' is given in the LHF files.

8.1 GLOSSARY OF FILE TYPES

FILE TYPE FORMAT DESCRIPTION CREATED BY SEE ALSO
Ligand hits file LHF format (FASTA-like). Database hits (sequences) with ligand classification information. The hits are putative ligand-binding sequences and are found from a search of a discriminating element (e.g. a protein signature) against a sequence database. SIGSCANLIG (hits retrieved by 1D and 3D signatures). N.A.
Signature alignment file SAF format (CLUSTAL-like). One or more signnature-sequence alignments, annotated with bibliographic information, either the domain family classification (for SIGSCAN output) or ligand classification (for SIGSCANLIG output). SIGSCAN (signature-sequence alignments for a single signature against a database of one or more sequences) or SIGSCANLIG (signature-sequence alignment for a single query sequence against a library of one or more signatures). N.A.
Signature file SIG format Contains a sparse sequence signature suitable for use with the SIGSCANLIG program. Contains a sparse sequence signature. SIGGEN, SIGGENLIG, LIBGEN The files are generated by using SIGGEN.



9.0 DESCRIPTION

SIGSCANLIG is an application to screen a query protein sequence against a library of signatures for ligand-binding. See Blades et al., Ison et al. and Daniel et al. for a description of other types of protein signatures and their application.


10.0 ALGORITHM

The algorithm is based on an approach first described in Daniel et al (1999) that was applied to the definition of protein families (Ison et al, 2000) and later to automatically-generated signatures (Blades et al, 2005).

Description of scoring modes
The user specifies the mode of scoring ligands, i.e. the way in which the scores in the results files are generated. In 'Patch Score Mode' (mode 1) the score for a ligand is the mean of its patch scores. In 'Site Score Mode' the score for a ligand is the mean of its site scores. A site score is the mean of patch score for all patches for a given site.

Selection of gap penalties
The user specifies the gap insertion and extension penalties. The gap insertion penalty is the score taken away when a gap is created. The gap extension penalty is added to the standard gap penalty for each base or residue in the gap. This is how long gaps are penalized. Usually you will expect a few long gaps rather than many short gaps, so the gap extension penalty should be lower than the gap penalty. The best value of these penalties depends on the choice of comparison matrix. The default value assumes you are using the EBLOSUM62 matrix for 1D signature scans. If you are performing 3D signature scans you should select a value appropriate to the scoring matrix used.


11.0 RELATED APPLICATIONS







11.0 RELATED APPLICATIONS

See also

Program name Description
profit Scan one or more sequences with a simple frequency matrix
prophecy Create frequency matrix or profile from a multiple alignment
prophet Scan one or more sequences with a Gribskov or Henikoff profile
seqsearch Generate PSI-BLAST hits (DHF file) from a DAF file
siggen Generates a sparse protein signature from an alignment
siggenlig Generates ligand-binding signatures from a CON file
sigscan Generates hits (DHF file) from a signature search



12.0 DIAGNOSTIC ERROR MESSAGES

None.


13.0 AUTHORS

Jon Ison (jison@ebi.ac.uk)

Waqas Awan
The European Bioinformatics Institute Wellcome Trust Genome Campus Cambridge CB10 1SD UK


14.0 REFERENCES

Automatic generation and evaluation of sparse protein signatures for families of protein structural domains. Blades MJ, Ison JC, Ranasinghe R and Findlay, JBC. Protein Science (2005), 14:13-23.

A key residues approach to the definition of protein families and analysis of sparse family signatures. JC Ison, AJ Bleasby, MJ Blades, SC Daniel, JH Parish, JBC Findlay. PROTEINS: Structure, Function & Genetics. 2000, 40:330-341

Alignment of a sparse protein signature with protein sequences: application to fold prediction for three small globulins. SC Daniel, JH Parish, JC Ison, MJ Blades & JBC Findlay. FEBS Letters. 1999, 459:349-352. Please cite the authors and EMBOSS.

Rice P, Longden I and Bleasby A (2000) "EMBOSS - The European Molecular Biology Open Software Suite" Trends in Genetics, 15:276-278.

See also http://emboss.sourceforge.net/

14.1 Other useful references