SIGGENLIG documentation |
XX Residue-ligand contact data (for domains). XX TY LIGAND XX EX THRESH 1.0; IGNORE .; NMOD .; NCHA .; XX NE 11 XX EN [1] XX ID PDB 1cs4; DOM d1cs4a_; LIG 101; XX DE 2'-DEOXY-ADENOSINE 3'-MONOPHOSPHATE XX SI SN 1; NS 2 XX CN MO .; CN1 1; CN2 .; ID1 A; ID2 .; NRES1 52; NRES2 . XX S1 SEQUENCE 52 AA; 5817 MW; D8CCAE0E1FC0849A CRC64; ADIEGFTSLA SQCTAQELVM TLNELFARFD KLAAENHCLR IKILGDCYYC VS XX NC SM .; LI 6 XX LI ASP 2 LI PHE 6 LI THR 7 LI LEU 44 LI GLY 45 LI ASP 46 XX // EN [2] XX ID PDB 1ii7; DOM d1ii7a_; LIG 101; XX DE 2'-DEOXY-ADENOSINE 3'-MONOPHOSPHATE XX SI SN 2; NS 2 XX CN MO .; CN1 1; CN2 .; ID1 A; ID2 .; NRES1 65; NRES2 . XX S1 SEQUENCE 65 AA; 7395 MW; 75FBE75B22FD3678 CRC64; MKFAHLADIH LGYEQFHKPQ REEEFAEAFK NALEIAVQEN VDFILIAGDL FHSSRPSPGT LKKAI XX NC SM .; LI 2 XX LI HIS 10 LI ASP 49 XX [Part of this file has been deleted for brevity] NC SM .; LI 3 XX LI ASP 8 LI HIS 10 LI ASP 49 XX // EN [10] XX ID PDB 2hhb; DOM .; LIG PO4; XX DE PHOSPHATE ION XX SI SN 1; NS 1 XX CN MO .; CN1 1; CN2 .; ID1 D; ID2 .; NRES1 146; NRES2 . XX S1 SEQUENCE 146 AA; 15867 MW; EACBC707CFD466A1 CRC64; VHLTPEEKSA VTALWGKVNV DEVGGEALGR LLVVYPWTQR FFESFGDLST PDAVMGNPKV KAHGKKVLGA FSDGLAHLDN LKGTFATLSE LHCDKLHVDP ENFRLLGNVL VCVLAHHFGK EFTPPVQAAY QKVVAGVANA LAHKYH XX NC SM .; LI 2 XX LI VAL 1 LI LEU 81 XX // EN [11] XX ID PDB 1cs4; DOM d1cs4a_; LIG POP; XX DE PYROPHOSPHATE 2- XX SI SN 1; NS 1 XX CN MO .; CN1 1; CN2 .; ID1 A; ID2 .; NRES1 52; NRES2 . XX S1 SEQUENCE 52 AA; 5817 MW; D8CCAE0E1FC0849A CRC64; ADIEGFTSLA SQCTAQELVM TLNELFARFD KLAAENHCLR IKILGDCYYC VS XX NC SM .; LI 6 XX LI ASP 2 LI ILE 3 LI GLU 4 LI GLY 5 LI PHE 6 LI THR 7 XX // |
TY LIGAND XX TS 1D XX ID PDB 1cs4; DOM d1cs4a_; LIG 101; XX DE 2'-DEOXY-ADENOSINE 3'-MONOPHOSPHATE XX IS SN 1; NS 2 XX IP PN 0; NP 0; MP 5; MG 2 XX NP 6 XX NN [1] XX IN NRES 1 ; NGAP 1 ; WSIZ 0 XX AA D ; 1 XX GA 1 ; 1 XX NN [2] XX IN NRES 1 ; NGAP 1 ; WSIZ 0 XX AA F ; 1 XX GA 3 ; 1 XX NN [3] XX IN NRES 1 ; NGAP 1 ; WSIZ 0 XX AA T ; 1 XX GA 0 ; 1 XX NN [4] XX IN NRES 1 ; NGAP 1 ; WSIZ 0 XX AA L ; 1 XX GA 36 ; 1 XX NN [5] XX IN NRES 1 ; NGAP 1 ; WSIZ 0 XX AA G ; 1 XX GA 0 ; 1 XX NN [6] XX IN NRES 1 ; NGAP 1 ; WSIZ 0 XX AA D ; 1 XX GA 0 ; 1 // |
TY LIGAND XX TS 1D XX ID PDB 1ii7; DOM d1ii7a_; LIG 101; XX DE 2'-DEOXY-ADENOSINE 3'-MONOPHOSPHATE XX IS SN 2; NS 2 XX IP PN 0; NP 0; MP 5; MG 2 XX NP 2 XX NN [1] XX IN NRES 1 ; NGAP 1 ; WSIZ 0 XX AA H ; 1 XX GA 9 ; 1 XX NN [2] XX IN NRES 1 ; NGAP 1 ; WSIZ 0 XX AA D ; 1 XX GA 38 ; 1 // |
TY LIGAND XX TS 1D XX ID PDB 1cs4; DOM d1cs4a_; LIG FOK; XX DE FORSKOLIN XX IS SN 1; NS 1 XX IP PN 0; NP 0; MP 5; MG 2 XX NP 1 XX NN [1] XX IN NRES 1 ; NGAP 1 ; WSIZ 0 XX AA L ; 1 XX GA 43 ; 1 // |
TY LIGAND XX TS 1D XX ID PDB 2hhb; DOM .; LIG HEM; XX DE PROTOPORPHYRIN IX CONTAINING FE XX IS SN 1; NS 4 XX IP PN 0; NP 0; MP 5; MG 2 XX NP 17 XX NN [1] XX IN NRES 1 ; NGAP 1 ; WSIZ 0 XX AA Y ; 1 XX GA 41 ; 1 XX NN [2] XX IN NRES 1 ; NGAP 1 ; WSIZ 0 XX AA F ; 1 XX GA 0 ; 1 XX NN [3] XX IN NRES 1 ; NGAP 1 ; WSIZ 0 XX AA H ; 1 XX GA 1 ; 1 XX NN [4] XX IN NRES 1 ; NGAP 1 ; WSIZ 0 XX AA F ; 1 XX GA 0 ; 1 XX NN [5] XX IN NRES 1 ; NGAP 1 ; WSIZ 0 XX [Part of this file has been deleted for brevity] XX GA 0 ; 1 XX NN [12] XX IN NRES 1 ; NGAP 1 ; WSIZ 0 XX AA L ; 1 XX GA 3 ; 1 XX NN [13] XX IN NRES 1 ; NGAP 1 ; WSIZ 0 XX AA V ; 1 XX GA 1 ; 1 XX NN [14] XX IN NRES 1 ; NGAP 1 ; WSIZ 0 XX AA N ; 1 XX GA 3 ; 1 XX NN [15] XX IN NRES 1 ; NGAP 1 ; WSIZ 0 XX AA F ; 1 XX GA 0 ; 1 XX NN [16] XX IN NRES 1 ; NGAP 1 ; WSIZ 0 XX AA L ; 1 XX GA 2 ; 1 XX NN [17] XX IN NRES 1 ; NGAP 1 ; WSIZ 0 XX AA L ; 1 XX GA 34 ; 1 // |
TY LIGAND XX TS 1D XX ID PDB 2hhb; DOM .; LIG HEM; XX DE PROTOPORPHYRIN IX CONTAINING FE XX IS SN 2; NS 4 XX IP PN 0; NP 0; MP 5; MG 2 XX NP 17 XX NN [1] XX IN NRES 1 ; NGAP 1 ; WSIZ 0 XX AA L ; 1 XX GA 30 ; 1 XX NN [2] XX IN NRES 1 ; NGAP 1 ; WSIZ 0 XX AA F ; 1 XX GA 9 ; 1 XX NN [3] XX IN NRES 1 ; NGAP 1 ; WSIZ 0 XX AA F ; 1 XX GA 0 ; 1 XX NN [4] XX IN NRES 1 ; NGAP 1 ; WSIZ 0 XX AA H ; 1 XX GA 20 ; 1 XX NN [5] XX IN NRES 1 ; NGAP 1 ; WSIZ 0 XX [Part of this file has been deleted for brevity] XX GA 0 ; 1 XX NN [12] XX IN NRES 1 ; NGAP 1 ; WSIZ 0 XX AA L ; 1 XX GA 3 ; 1 XX NN [13] XX IN NRES 1 ; NGAP 1 ; WSIZ 0 XX AA V ; 1 XX GA 1 ; 1 XX NN [14] XX IN NRES 1 ; NGAP 1 ; WSIZ 0 XX AA N ; 1 XX GA 3 ; 1 XX NN [15] XX IN NRES 1 ; NGAP 1 ; WSIZ 0 XX AA F ; 1 XX GA 0 ; 1 XX NN [16] XX IN NRES 1 ; NGAP 1 ; WSIZ 0 XX AA L ; 1 XX GA 2 ; 1 XX NN [17] XX IN NRES 1 ; NGAP 1 ; WSIZ 0 XX AA L ; 1 XX GA 34 ; 1 // |
TY LIGAND XX TS 1D XX ID PDB 2hhb; DOM .; LIG HEM; XX DE PROTOPORPHYRIN IX CONTAINING FE XX IS SN 3; NS 4 XX IP PN 0; NP 0; MP 5; MG 2 XX NP 19 XX NN [1] XX IN NRES 1 ; NGAP 1 ; WSIZ 0 XX AA M ; 1 XX GA 31 ; 1 XX NN [2] XX IN NRES 1 ; NGAP 1 ; WSIZ 0 XX AA T ; 1 XX GA 6 ; 1 XX NN [3] XX IN NRES 1 ; NGAP 1 ; WSIZ 0 XX AA Y ; 1 XX GA 2 ; 1 XX NN [4] XX IN NRES 1 ; NGAP 1 ; WSIZ 0 XX AA F ; 1 XX GA 0 ; 1 XX NN [5] XX IN NRES 1 ; NGAP 1 ; WSIZ 0 XX [Part of this file has been deleted for brevity] XX GA 0 ; 1 XX NN [14] XX IN NRES 1 ; NGAP 1 ; WSIZ 0 XX AA L ; 1 XX GA 3 ; 1 XX NN [15] XX IN NRES 1 ; NGAP 1 ; WSIZ 0 XX AA V ; 1 XX GA 1 ; 1 XX NN [16] XX IN NRES 1 ; NGAP 1 ; WSIZ 0 XX AA N ; 1 XX GA 3 ; 1 XX NN [17] XX IN NRES 1 ; NGAP 1 ; WSIZ 0 XX AA F ; 1 XX GA 0 ; 1 XX NN [18] XX IN NRES 1 ; NGAP 1 ; WSIZ 0 XX AA L ; 1 XX GA 2 ; 1 XX NN [19] XX IN NRES 1 ; NGAP 1 ; WSIZ 0 XX AA L ; 1 XX GA 34 ; 1 // |
TY LIGAND XX TS 1D XX ID PDB 2hhb; DOM .; LIG HEM; XX DE PROTOPORPHYRIN IX CONTAINING FE XX IS SN 4; NS 4 XX IP PN 0; NP 0; MP 5; MG 2 XX NP 15 XX NN [1] XX IN NRES 1 ; NGAP 1 ; WSIZ 0 XX AA L ; 1 XX GA 30 ; 1 XX NN [2] XX IN NRES 1 ; NGAP 1 ; WSIZ 0 XX AA F ; 1 XX GA 9 ; 1 XX NN [3] XX IN NRES 1 ; NGAP 1 ; WSIZ 0 XX AA F ; 1 XX GA 0 ; 1 XX NN [4] XX IN NRES 1 ; NGAP 1 ; WSIZ 0 XX AA H ; 1 XX GA 20 ; 1 XX NN [5] XX IN NRES 1 ; NGAP 1 ; WSIZ 0 XX [Part of this file has been deleted for brevity] XX GA 0 ; 1 XX NN [10] XX IN NRES 1 ; NGAP 1 ; WSIZ 0 XX AA L ; 1 XX GA 3 ; 1 XX NN [11] XX IN NRES 1 ; NGAP 1 ; WSIZ 0 XX AA V ; 1 XX GA 1 ; 1 XX NN [12] XX IN NRES 1 ; NGAP 1 ; WSIZ 0 XX AA N ; 1 XX GA 3 ; 1 XX NN [13] XX IN NRES 1 ; NGAP 1 ; WSIZ 0 XX AA F ; 1 XX GA 0 ; 1 XX NN [14] XX IN NRES 1 ; NGAP 1 ; WSIZ 0 XX AA L ; 1 XX GA 2 ; 1 XX NN [15] XX IN NRES 1 ; NGAP 1 ; WSIZ 0 XX AA L ; 1 XX GA 34 ; 1 // |
TY LIGAND XX TS 1D XX ID PDB 1cs4; DOM d1cs4a_; LIG MG; XX DE MAGNESIUM ION XX IS SN 1; NS 1 XX IP PN 0; NP 0; MP 5; MG 2 XX NP 4 XX NN [1] XX IN NRES 1 ; NGAP 1 ; WSIZ 0 XX AA D ; 1 XX GA 1 ; 1 XX NN [2] XX IN NRES 1 ; NGAP 1 ; WSIZ 0 XX AA I ; 1 XX GA 0 ; 1 XX NN [3] XX IN NRES 1 ; NGAP 1 ; WSIZ 0 XX AA F ; 1 XX GA 2 ; 1 XX NN [4] XX IN NRES 1 ; NGAP 1 ; WSIZ 0 XX AA D ; 1 XX GA 39 ; 1 // |
TY LIGAND XX TS 1D XX ID PDB 1ii7; DOM d1ii7a_; LIG MN; XX DE MANGANESE (II) ION XX IS SN 1; NS 1 XX IP PN 0; NP 0; MP 5; MG 2 XX NP 3 XX NN [1] XX IN NRES 1 ; NGAP 1 ; WSIZ 0 XX AA D ; 1 XX GA 7 ; 1 XX NN [2] XX IN NRES 1 ; NGAP 1 ; WSIZ 0 XX AA H ; 1 XX GA 1 ; 1 XX NN [3] XX IN NRES 1 ; NGAP 1 ; WSIZ 0 XX AA D ; 1 XX GA 38 ; 1 // |
TY LIGAND XX TS 1D XX ID PDB 2hhb; DOM .; LIG PO4; XX DE PHOSPHATE ION XX IS SN 1; NS 1 XX IP PN 0; NP 0; MP 5; MG 2 XX NP 2 XX NN [1] XX IN NRES 1 ; NGAP 1 ; WSIZ 0 XX AA V ; 1 XX GA 0 ; 1 XX NN [2] XX IN NRES 1 ; NGAP 1 ; WSIZ 0 XX AA L ; 1 XX GA 79 ; 1 // |
TY LIGAND XX TS 1D XX ID PDB 1cs4; DOM d1cs4a_; LIG POP; XX DE PYROPHOSPHATE 2- XX IS SN 1; NS 1 XX IP PN 0; NP 0; MP 5; MG 2 XX NP 6 XX NN [1] XX IN NRES 1 ; NGAP 1 ; WSIZ 0 XX AA D ; 1 XX GA 1 ; 1 XX NN [2] XX IN NRES 1 ; NGAP 1 ; WSIZ 0 XX AA I ; 1 XX GA 0 ; 1 XX NN [3] XX IN NRES 1 ; NGAP 1 ; WSIZ 0 XX AA E ; 1 XX GA 0 ; 1 XX NN [4] XX IN NRES 1 ; NGAP 1 ; WSIZ 0 XX AA G ; 1 XX GA 0 ; 1 XX NN [5] XX IN NRES 1 ; NGAP 1 ; WSIZ 0 XX AA F ; 1 XX GA 0 ; 1 XX NN [6] XX IN NRES 1 ; NGAP 1 ; WSIZ 0 XX AA T ; 1 XX GA 0 ; 1 // |
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Generates ligand-binding signatures from a CON file Version: EMBOSS:6.4.0.0 Standard (Mandatory) qualifiers (* if not always prompted): [-confile] infile This option specifies the name of the CON file (contact file) (input). A 'contact file' contains contact data for a protein or a domain from SCOP or CATH, in the CON format (EMBL-like). The contacts may be intra-chain residue-residue, inter-chain residue-residue or residue-ligand. The files are generated by using CONTACTS, INTERFACE and SITES. -ccfpdir directory This option specifies the location of protein CCF file (clean coordinate files) (input). A 'clean cordinate file' contains protein coordinate and derived data for a single PDB file ('protein clean coordinate file') or a single domain from SCOP or CATH ('domain clean coordinate file'), in CCF format (EMBL-like). The files, generated by using PDBPARSE (PDB files) or DOMAINER (domains), contain 'cleaned-up' data that is self-consistent and error-corrected. Records for residue solvent accessibility and secondary structure are added to the file by using PDBPLUS. default: ./ -ccfddir directory This option specifies the location of protein CCF file (clean coordinate files) (input). A 'clean cordinate file' contains protein coordinate and derived data for a single PDB file ('protein clean coordinate file') or a single domain from SCOP or CATH ('domain clean coordinate file'), in CCF format (EMBL-like). The files, generated by using PDBPARSE (PDB files) or DOMAINER (domains), contain 'cleaned-up' data that is self-consistent and error-corrected. Records for residue solvent accessibility and secondary structure are added to the file by using PDBPLUS. default: ./ -mode menu [1] This option specifies the mode of signature generation. In 'Full-length signature mode' (mode 1) a single signature incorporating all residue positions that contact the ligand plus intervening gaps is generated. In 'Patch signature mode' (mode 2) one or more signatures corresponding to 'patches' of residue positions are generated. A patch is a set of residues that are near-neighbours in sequence and is described by two user-defined parameters: minimum patch size and maximum gap distance. (Values: 1 (Full-length signature mode); 2 (Patch signature mode)) -type menu [1] This option specifies the type of signature generated. In '1D (sequence) signature' sequence-based signatures are generated. In '3D (structural) signature' structure-based signatures are generated. (Values: 1 (1D (sequence) signature); 2 (3D (structural) signature)) * -patchsize integer [5] This option specifies the minimum patch size. This is the minimum number of contact positions that must be incorporated in a signature. (Integer 3 or more) * -gapdistance integer [2] This option specifies the maximum gap distance. This is the maximum allowable gap (residues) between two residue in a patch. If two contact residues are further than this distance apart in sequence, they would not belong to the same patch. (Integer 0 or more) * -environment menu [1] This option specifies the environment definition. See matgen3d documentation for description of definitions. (Values: 1 (Env1); 2 (Env2); 3 (Env3); 4 (Env4); 5 (Env5); 6 (Env6); 7 (Env7); 8 (Env8); 9 (Env9); 10 (Env10); 11 (Env11); 12 (Env12); 13 (Env13); 14 (Env14); 15 (Env15); 16 (Env16)) [-sigoutdir] outdir [./] This option specifies the location of signature files (output). 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. [-logfile] outfile [siggenlig.log] Domainatrix log output file Additional (Optional) qualifiers: (none) Advanced (Unprompted) qualifiers: (none) Associated qualifiers: "-ccfpdir" associated qualifiers -extension string Default file extension "-ccfddir" associated qualifiers -extension string Default file extension "-sigoutdir" associated qualifiers -extension2 string Default file extension "-logfile" associated qualifiers -odirectory3 string Output directory 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 |
Qualifier | Type | Description | Allowed values | Default | ||||||||||||||||||||||||||||||||
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Standard (Mandatory) qualifiers | ||||||||||||||||||||||||||||||||||||
[-confile] (Parameter 1) |
infile | This option specifies the name of the CON file (contact file) (input). A 'contact file' contains contact data for a protein or a domain from SCOP or CATH, in the CON format (EMBL-like). The contacts may be intra-chain residue-residue, inter-chain residue-residue or residue-ligand. The files are generated by using CONTACTS, INTERFACE and SITES. | Input file | Required | ||||||||||||||||||||||||||||||||
-ccfpdir | directory | This option specifies the location of protein CCF file (clean coordinate files) (input). A 'clean cordinate file' contains protein coordinate and derived data for a single PDB file ('protein clean coordinate file') or a single domain from SCOP or CATH ('domain clean coordinate file'), in CCF format (EMBL-like). The files, generated by using PDBPARSE (PDB files) or DOMAINER (domains), contain 'cleaned-up' data that is self-consistent and error-corrected. Records for residue solvent accessibility and secondary structure are added to the file by using PDBPLUS. default: ./ | Directory | |||||||||||||||||||||||||||||||||
-ccfddir | directory | This option specifies the location of protein CCF file (clean coordinate files) (input). A 'clean cordinate file' contains protein coordinate and derived data for a single PDB file ('protein clean coordinate file') or a single domain from SCOP or CATH ('domain clean coordinate file'), in CCF format (EMBL-like). The files, generated by using PDBPARSE (PDB files) or DOMAINER (domains), contain 'cleaned-up' data that is self-consistent and error-corrected. Records for residue solvent accessibility and secondary structure are added to the file by using PDBPLUS. default: ./ | Directory | |||||||||||||||||||||||||||||||||
-mode | list | This option specifies the mode of signature generation. In 'Full-length signature mode' (mode 1) a single signature incorporating all residue positions that contact the ligand plus intervening gaps is generated. In 'Patch signature mode' (mode 2) one or more signatures corresponding to 'patches' of residue positions are generated. A patch is a set of residues that are near-neighbours in sequence and is described by two user-defined parameters: minimum patch size and maximum gap distance. |
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1 | ||||||||||||||||||||||||||||||||
-type | list | This option specifies the type of signature generated. In '1D (sequence) signature' sequence-based signatures are generated. In '3D (structural) signature' structure-based signatures are generated. |
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1 | ||||||||||||||||||||||||||||||||
-patchsize | integer | This option specifies the minimum patch size. This is the minimum number of contact positions that must be incorporated in a signature. | Integer 3 or more | 5 | ||||||||||||||||||||||||||||||||
-gapdistance | integer | This option specifies the maximum gap distance. This is the maximum allowable gap (residues) between two residue in a patch. If two contact residues are further than this distance apart in sequence, they would not belong to the same patch. | Integer 0 or more | 2 | ||||||||||||||||||||||||||||||||
-environment | list | This option specifies the environment definition. See matgen3d documentation for description of definitions. |
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1 | ||||||||||||||||||||||||||||||||
[-sigoutdir] (Parameter 2) |
outdir | This option specifies the location of signature files (output). 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. | Output directory | ./ | ||||||||||||||||||||||||||||||||
[-logfile] (Parameter 3) |
outfile | Domainatrix log output file | Output file | siggenlig.log | ||||||||||||||||||||||||||||||||
Additional (Optional) qualifiers | ||||||||||||||||||||||||||||||||||||
(none) | ||||||||||||||||||||||||||||||||||||
Advanced (Unprompted) qualifiers | ||||||||||||||||||||||||||||||||||||
(none) | ||||||||||||||||||||||||||||||||||||
Associated qualifiers | ||||||||||||||||||||||||||||||||||||
"-ccfpdir" associated directory qualifiers | ||||||||||||||||||||||||||||||||||||
-extension | string | Default file extension | Any string | ccf | ||||||||||||||||||||||||||||||||
"-ccfddir" associated directory qualifiers | ||||||||||||||||||||||||||||||||||||
-extension | string | Default file extension | Any string | ccf | ||||||||||||||||||||||||||||||||
"-sigoutdir" associated outdir qualifiers | ||||||||||||||||||||||||||||||||||||
-extension2 -extension_sigoutdir |
string | Default file extension | Any string | sig | ||||||||||||||||||||||||||||||||
"-logfile" associated outfile qualifiers | ||||||||||||||||||||||||||||||||||||
-odirectory3 -odirectory_logfile |
string | Output directory | Any string | |||||||||||||||||||||||||||||||||
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 |
% siggenlig Generates ligand-binding signatures from a CON file Structure contacts file: ../sites-keep/SITES.con Clean protein structure coordinates directory (optional) [.]: ../pdbplus-keep Clean domain coordinates directory (optional) [.]: ../domainer-keep Available modes 1 : Full-length signature mode 2 : Patch signature mode Select mode of operation. [1]: 1 Available types 1 : 1D (sequence) signature 2 : 3D (structural) signature Select type of signature. [1]: 1 Domainatrix signature file output directory [./]: Domainatrix log output file [siggenlig.log]: |
Go to the input files for this example
Go to the output files for this example
FILE TYPE | FORMAT | DESCRIPTION | CREATED BY | SEE ALSO |
Clean coordinate file (for domain) | CCF format (EMBL-like). | Protein coordinate and derived data for a single domain from SCOP or CATH. The data are 'cleaned-up': self-consistent and error-corrected. | DOMAINER | Records for residue solvent accessibility and secondary structure are added to the file by using PDBPLUS. |
Clean coordinate file (for domain) | CCF format (EMBL-like). | Protein coordinate and derived data for a single domain from SCOP or CATH. The data are 'cleaned-up': self-consistent and error-corrected. | DOMAINER | Records for residue solvent accessibility and secondary structure are added to the file by using PDBPLUS. |
Contact file (residue-ligand contacts) | CON format (EMBL-like.) | Residue-ligand contact data for a protein or a domain from SCOP or CATH. | SITES | N.A. |
Signature file | SIG format | Contains a sparse sequence signature suitable for use with the SIGSCAN program. Contains a sparse sequence signature. | SIGGEN, LIBGEN | The files are generated by using SIGGENLIG. |
Program name | Description |
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echlorop | Reports presence of chloroplast transit peptides |
elipop | Prediction of lipoproteins |
esignalp | Reports protein signal cleavage sites |
etmhmm | Reports transmembrane helices |
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 |
sigcleave | Reports on signal cleavage sites in a protein sequence |
siggen | Generates a sparse protein signature from an alignment |
sigscan | Generates hits (DHF file) from a signature search |
sigscanlig | Searches ligand-signature library and writes hits (LHF file) |
tmap | Predict and plot transmembrane segments in protein sequences |
topo | Draws an image of a transmembrane protein |
See also http://emboss.sourceforge.net/