Appdoc:Dotmatcher

From EMBOSS

Contents 1 Function 2 Description 3 Algorithm 4 Usage 5 Command line arguments 6 Input file format 6.1 Input example 6.1.1 Database entry: tsw:hba_human 6.1.2 Database entry: tsw:hbb_human 7 Output file format 7.1 Output example 7.1.1 Graphics File: dotmatcher.ps 8 Data files 9 Notes 10 References 11 Warnings 12 Diagnostic Error Messages 13 Exit status 14 Known bugs 15 See also 16 Author(s) 17 History 18 Target users 19 Comments

Function

Draw a threshold dotplot of two sequences

Description

dotmatcher generates a dotplot from two input sequences. The dotplot is an intuitive graphical representation of the regions of similarity between two sequences. All positions from the first input sequence are compared with all positions from the second input sequence using a specified substitution matrix. The two sequences are the axes of the rectangular dotplot. Wherever there is "similarity" between a position from each sequence a dot is plotted. The threshold conditions for "similarity" are defined by the user.

Algorithm

All positions from the first input sequence are compared with all positions from the second input sequence and scored, using the specified substitution matrix. This produces a matrix of scores from which local regions of similarity (corresponding to diagonals in the dotplot) are identified. A window of user-specified length is moved along all possible diagonals. Each position in the window corresponds to a pair-wise score from the scoring matrix. The score for the entire window is the sum of the scores for individual positions within it. If the window score is above the user-defined threshold, then a line is plotted on the dotplot corresponding to the window.

Usage

Here is a sample session with dotmatcher

% dotmatcher tsw:hba_human tsw:hbb_human -graph cps 
Draw a threshold dotplot of two sequences

Created dotmatcher.ps

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

Command line arguments

Qualifier	Type	Description	Allowed values	Default
Standard (Mandatory) qualifiers
[-asequence] (Parameter 1)	sequence	Sequence filename and optional format, or reference (input USA)	Readable sequence	Required
[-bsequence] (Parameter 2)	sequence	Sequence filename and optional format, or reference (input USA)	Readable sequence	Required
-graph	graph	Graph type	EMBOSS has a list of known devices, including ps, hpgl, hp7470, hp7580, meta, cps, x11, tekt, tek, none, data, das, xterm, png, gif	EMBOSS_GRAPHICS value, or x11
-xygraph	xygraph	Graph type	EMBOSS has a list of known devices, including ps, hpgl, hp7470, hp7580, meta, cps, x11, tekt, tek, none, data, das, xterm, png, gif	EMBOSS_GRAPHICS value, or x11
Additional (Optional) qualifiers
-matrixfile	matrix	This is the scoring matrix file used when comparing sequences. By default it is the file 'EBLOSUM62' (for proteins) or the file 'EDNAFULL' (for nucleic sequences). These files are found in the 'data' directory of the EMBOSS installation.	Comparison matrix file in EMBOSS data path	EBLOSUM62 for protein EDNAFULL for DNA
-windowsize	integer	Window size over which to test threshhold	Integer 3 or more	10
-threshold	integer	Threshold	Integer 0 or more	23
Advanced (Unprompted) qualifiers
-stretch	toggle	Display a non-proportional graph	Toggle value Yes/No	No
Associated qualifiers
"-asequence" associated sequence qualifiers
-sbegin1 -sbegin_asequence	integer	Start of the sequence to be used	Any integer value	0
-send1 -send_asequence	integer	End of the sequence to be used	Any integer value	0
-sreverse1 -sreverse_asequence	boolean	Reverse (if DNA)	Boolean value Yes/No	N
-sask1 -sask_asequence	boolean	Ask for begin/end/reverse	Boolean value Yes/No	N
-snucleotide1 -snucleotide_asequence	boolean	Sequence is nucleotide	Boolean value Yes/No	N
-sprotein1 -sprotein_asequence	boolean	Sequence is protein	Boolean value Yes/No	N
-slower1 -slower_asequence	boolean	Make lower case	Boolean value Yes/No	N
-supper1 -supper_asequence	boolean	Make upper case	Boolean value Yes/No	N
-sformat1 -sformat_asequence	string	Input sequence format	Any string
-sdbname1 -sdbname_asequence	string	Database name	Any string
-sid1 -sid_asequence	string	Entryname	Any string
-ufo1 -ufo_asequence	string	UFO features	Any string
-fformat1 -fformat_asequence	string	Features format	Any string
-fopenfile1 -fopenfile_asequence	string	Features file name	Any string
"-bsequence" associated sequence qualifiers
-sbegin2 -sbegin_bsequence	integer	Start of the sequence to be used	Any integer value	0
-send2 -send_bsequence	integer	End of the sequence to be used	Any integer value	0
-sreverse2 -sreverse_bsequence	boolean	Reverse (if DNA)	Boolean value Yes/No	N
-sask2 -sask_bsequence	boolean	Ask for begin/end/reverse	Boolean value Yes/No	N
-snucleotide2 -snucleotide_bsequence	boolean	Sequence is nucleotide	Boolean value Yes/No	N
-sprotein2 -sprotein_bsequence	boolean	Sequence is protein	Boolean value Yes/No	N
-slower2 -slower_bsequence	boolean	Make lower case	Boolean value Yes/No	N
-supper2 -supper_bsequence	boolean	Make upper case	Boolean value Yes/No	N
-sformat2 -sformat_bsequence	string	Input sequence format	Any string
-sdbname2 -sdbname_bsequence	string	Database name	Any string
-sid2 -sid_bsequence	string	Entryname	Any string
-ufo2 -ufo_bsequence	string	UFO features	Any string
-fformat2 -fformat_bsequence	string	Features format	Any string
-fopenfile2 -fopenfile_bsequence	string	Features file name	Any string
"-graph" associated graph qualifiers
-gprompt	boolean	Graph prompting	Boolean value Yes/No	N
-gdesc	string	Graph description	Any string
-gtitle	string	Graph title	Any string	Dotmatcher: $(asequence.usa) vs $(bsequence.usa)
-gsubtitle	string	Graph subtitle	Any string
-gxtitle	string	Graph x axis title	Any string	$(asequence.name)
-gytitle	string	Graph y axis title	Any string	$(bsequence.name)
-goutfile	string	Output file for non interactive displays	Any string
-gdirectory	string	Output directory	Any string
"-xygraph" associated xygraph qualifiers
-gprompt	boolean	Graph prompting	Boolean value Yes/No	N
-gdesc	string	Graph description	Any string
-gtitle	string	Graph title	Any string	Dotmatcher: $(asequence.usa) vs $(bsequence.usa)
-gsubtitle	string	Graph subtitle	Any string
-gxtitle	string	Graph x axis title	Any string	$(asequence.name)
-gytitle	string	Graph y axis title	Any string	$(bsequence.name)
-goutfile	string	Output file for non interactive displays	Any string
-gdirectory	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. 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

Input file format

Any 2 sequence USAs of the same type (DNA or protein).

Input example

'tsw:hba_human' is a sequence entry in the example protein database 'tsw'

Database entry: tsw:hba_human

ID   HBA_HUMAN               Reviewed;         142 AA.
AC   P69905; P01922; Q1HDT5; Q3MIF5; Q53F97; Q96KF1; Q9NYR7; Q9UCM0;
DT   21-JUL-1986, integrated into UniProtKB/Swiss-Prot.
DT   23-JAN-2007, sequence version 2.
DT   16-JUN-2009, entry version 73.
DE   RecName: Full=Hemoglobin subunit alpha;
DE   AltName: Full=Hemoglobin alpha chain;
DE   AltName: Full=Alpha-globin;
GN   Name=HBA1;
GN   and
GN   Name=HBA2;
OS   Homo sapiens (Human).
OC   Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi;
OC   Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini;
OC   Catarrhini; Hominidae; Homo.
OX   NCBI_TaxID=9606;
RN   [1]
RP   NUCLEOTIDE SEQUENCE [GENOMIC DNA] (HBA1).
RX   MEDLINE=81088339; PubMed=7448866; DOI=10.1016/0092-8674(80)90347-5;
RA   Michelson A.M., Orkin S.H.;
RT   "The 3' untranslated regions of the duplicated human alpha-globin
RT   genes are unexpectedly divergent.";
RL   Cell 22:371-377(1980).
RN   [2]
RP   NUCLEOTIDE SEQUENCE [MRNA] (HBA2).
RX   MEDLINE=80137531; PubMed=6244294;
RA   Wilson J.T., Wilson L.B., Reddy V.B., Cavallesco C., Ghosh P.K.,
RA   Deriel J.K., Forget B.G., Weissman S.M.;
RT   "Nucleotide sequence of the coding portion of human alpha globin
RT   messenger RNA.";
RL   J. Biol. Chem. 255:2807-2815(1980).
RN   [3]
RP   NUCLEOTIDE SEQUENCE [GENOMIC DNA] (HBA2).
RX   MEDLINE=81175088; PubMed=6452630; DOI=10.1073/pnas.77.12.7054;
RA   Liebhaber S.A., Goossens M.J., Kan Y.W.;
RT   "Cloning and complete nucleotide sequence of human 5'-alpha-globin
RT   gene.";
RL   Proc. Natl. Acad. Sci. U.S.A. 77:7054-7058(1980).
RN   [4]
RP   NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RX   PubMed=6946451; DOI=10.1073/pnas.78.8.5041;
RA   Orkin S.H., Goff S.C., Hechtman R.L.;
RT   "Mutation in an intervening sequence splice junction in man.";
RL   Proc. Natl. Acad. Sci. U.S.A. 78:5041-5045(1981).
RN   [5]
RP   NUCLEOTIDE SEQUENCE [GENOMIC DNA], AND VARIANT LYS-32.
RX   MEDLINE=21303311; PubMed=11410421;
RA   Zhao Y., Xu X.;
RT   "Alpha2(CD31 AGG-->AAG, Arg-->Lys) causing non-deletional alpha-
RT   thalassemia in a Chinese family with HbH disease.";


  [Part of this file has been deleted for brevity]

FT                                /FTId=VAR_002841.
FT   VARIANT     132    132       S -> P (in Questembert; highly unstable;
FT                                causes alpha-thalassemia).
FT                                /FTId=VAR_002843.
FT   VARIANT     134    134       S -> R (in Val de Marne; O(2) affinity
FT                                up).
FT                                /FTId=VAR_002844.
FT   VARIANT     136    136       V -> E (in Pavie).
FT                                /FTId=VAR_002845.
FT   VARIANT     137    137       L -> M (in Chicago).
FT                                /FTId=VAR_002846.
FT   VARIANT     137    137       L -> P (in Bibba; unstable; causes alpha-
FT                                thalassemia).
FT                                /FTId=VAR_002847.
FT   VARIANT     137    137       L -> R (in Toyama).
FT                                /FTId=VAR_035242.
FT   VARIANT     139    139       S -> P (in Attleboro; O(2) affinity up).
FT                                /FTId=VAR_002848.
FT   VARIANT     140    140       K -> E (in Hanamaki; O(2) affinity up).
FT                                /FTId=VAR_002849.
FT   VARIANT     140    140       K -> T (in Tokoname; O(2) affinity up).
FT                                /FTId=VAR_002850.
FT   VARIANT     141    141       Y -> H (in Rouen/Ethiopia; O(2) affinity
FT                                up).
FT                                /FTId=VAR_002851.
FT   VARIANT     142    142       R -> C (in Nunobiki; O(2) affinity up).
FT                                /FTId=VAR_002852.
FT   VARIANT     142    142       R -> H (in Suresnes; O(2) affinity up).
FT                                /FTId=VAR_002854.
FT   VARIANT     142    142       R -> L (in Legnano; O(2) affinity up).
FT                                /FTId=VAR_002853.
FT   VARIANT     142    142       R -> P (in Singapore).
FT                                /FTId=VAR_002855.
FT   CONFLICT     10     10       N -> H (in Ref. 13; BAD97112).
FT   HELIX         5     16
FT   HELIX        17     21
FT   HELIX        22     36
FT   HELIX        38     43
FT   HELIX        54     72
FT   HELIX        74     76
FT   HELIX        77     80
FT   HELIX        82     90
FT   HELIX        97    113
FT   TURN        115    117
FT   HELIX       120    137
FT   TURN        138    140
SQ   SEQUENCE   142 AA;  15258 MW;  15E13666573BBBAE CRC64;
     MVLSPADKTN VKAAWGKVGA HAGEYGAEAL ERMFLSFPTT KTYFPHFDLS HGSAQVKGHG
     KKVADALTNA VAHVDDMPNA LSALSDLHAH KLRVDPVNFK LLSHCLLVTL AAHLPAEFTP
     AVHASLDKFL ASVSTVLTSK YR
//

Database entry: tsw:hbb_human

ID   HBB_HUMAN               Reviewed;         147 AA.
AC   P68871; A4GX73; B2ZUE0; P02023; Q13852; Q14481; Q14510; Q45KT0;
AC   Q549N7; Q6FI08; Q6R7N2; Q8IZI1; Q9BX96; Q9UCD6; Q9UCP8; Q9UCP9;
DT   21-JUL-1986, integrated into UniProtKB/Swiss-Prot.
DT   23-JAN-2007, sequence version 2.
DT   16-JUN-2009, entry version 76.
DE   RecName: Full=Hemoglobin subunit beta;
DE   AltName: Full=Hemoglobin beta chain;
DE   AltName: Full=Beta-globin;
DE   Contains:
DE     RecName: Full=LVV-hemorphin-7;
GN   Name=HBB;
OS   Homo sapiens (Human).
OC   Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi;
OC   Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini;
OC   Catarrhini; Hominidae; Homo.
OX   NCBI_TaxID=9606;
RN   [1]
RP   NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RX   MEDLINE=77126403; PubMed=1019344;
RA   Marotta C., Forget B., Cohen-Solal M., Weissman S.M.;
RT   "Nucleotide sequence analysis of coding and noncoding regions of human
RT   beta-globin mRNA.";
RL   Prog. Nucleic Acid Res. Mol. Biol. 19:165-175(1976).
RN   [2]
RP   NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RX   MEDLINE=81064667; PubMed=6254664; DOI=10.1016/0092-8674(80)90428-6;
RA   Lawn R.M., Efstratiadis A., O'Connell C., Maniatis T.;
RT   "The nucleotide sequence of the human beta-globin gene.";
RL   Cell 21:647-651(1980).
RN   [3]
RP   NUCLEOTIDE SEQUENCE [GENOMIC DNA], AND VARIANT LYS-7.
RX   PubMed=16175509; DOI=10.1086/491748;
RA   Wood E.T., Stover D.A., Slatkin M., Nachman M.W., Hammer M.F.;
RT   "The beta-globin recombinational hotspot reduces the effects of strong
RT   selection around HbC, a recently arisen mutation providing resistance
RT   to malaria.";
RL   Am. J. Hum. Genet. 77:637-642(2005).
RN   [4]
RP   NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RA   Lu L., Hu Z.H., Du C.S., Fu Y.S.;
RT   "DNA sequence of the human beta-globin gene isolated from a healthy
RT   Chinese.";
RL   Submitted (JUN-1997) to the EMBL/GenBank/DDBJ databases.
RN   [5]
RP   NUCLEOTIDE SEQUENCE [GENOMIC DNA], AND VARIANT ARG-113.
RA   Cabeda J.M., Correia C., Estevinho A., Cardoso C., Amorim M.L.,
RA   Cleto E., Vale L., Coimbra E., Pinho L., Justica B.;
RT   "Unexpected patterns of globin mutations in thalassemia patients from
RT   north of Portugal.";


  [Part of this file has been deleted for brevity]

FT   VARIANT     141    141       A -> V (in Puttelange; polycythemia; O(2)
FT                                affinity up).
FT                                /FTId=VAR_003082.
FT   VARIANT     142    142       L -> R (in Olmsted; unstable).
FT                                /FTId=VAR_003083.
FT   VARIANT     143    143       A -> D (in Ohio; O(2) affinity up).
FT                                /FTId=VAR_003084.
FT   VARIANT     144    144       H -> D (in Rancho Mirage).
FT                                /FTId=VAR_003085.
FT   VARIANT     144    144       H -> P (in Syracuse; O(2) affinity up).
FT                                /FTId=VAR_003087.
FT   VARIANT     144    144       H -> Q (in Little Rock; O(2) affinity
FT                                up).
FT                                /FTId=VAR_003086.
FT   VARIANT     144    144       H -> R (in Abruzzo; O(2) affinity up).
FT                                /FTId=VAR_003088.
FT   VARIANT     145    145       K -> E (in Mito; O(2) affinity up).
FT                                /FTId=VAR_003089.
FT   VARIANT     146    146       Y -> C (in Rainier; O(2) affinity up).
FT                                /FTId=VAR_003090.
FT   VARIANT     146    146       Y -> H (in Bethesda; O(2) affinity up).
FT                                /FTId=VAR_003091.
FT   VARIANT     147    147       H -> D (in Hiroshima; O(2) affinity up).
FT                                /FTId=VAR_003092.
FT   VARIANT     147    147       H -> L (in Cowtown; O(2) affinity up).
FT                                /FTId=VAR_003093.
FT   VARIANT     147    147       H -> P (in York; O(2) affinity up).
FT                                /FTId=VAR_003094.
FT   VARIANT     147    147       H -> Q (in Kodaira; O(2) affinity up).
FT                                /FTId=VAR_003095.
FT   CONFLICT     26     26       Missing (in Ref. 15; ACD39349).
FT   CONFLICT     42     42       F -> L (in Ref. 13; AAR96398).
FT   HELIX         6     16
FT   TURN         21     23
FT   HELIX        24     35
FT   HELIX        37     42
FT   HELIX        44     46
FT   HELIX        52     57
FT   HELIX        59     77
FT   TURN         78     80
FT   HELIX        82     94
FT   TURN         95     97
FT   HELIX       102    119
FT   HELIX       120    122
FT   HELIX       125    142
FT   HELIX       144    146
SQ   SEQUENCE   147 AA;  15998 MW;  A31F6D621C6556A1 CRC64;
     MVHLTPEEKS AVTALWGKVN VDEVGGEALG RLLVVYPWTQ RFFESFGDLS TPDAVMGNPK
     VKAHGKKVLG AFSDGLAHLD NLKGTFATLS ELHCDKLHVD PENFRLLGNV LVCVLAHHFG
     KEFTPPVQAA YQKVVAGVAN ALAHKYH
//

Output file format

An image is output to the requested graphics device.

Output example

Graphics File: dotmatcher.ps

Data files

It uses the specified matrix substitution file to compare the two sequences.

For protein sequences EBLOSUM62 is used for the substitution matrix. For nucleotide sequence, EDNAFULL is used. Others can be specified.

EMBOSS data files are distributed with the application and stored in the standard EMBOSS data directory, which is defined by the EMBOSS environment variable EMBOSS_DATA.

To see the available EMBOSS data files, run:

% embossdata -showall

To fetch one of the data files (for example 'Exxx.dat') into your current directory for you to inspect or modify, run:

% embossdata -fetch -file Exxx.dat

Users can provide their own data files in their own directories. Project specific files can be put in the current directory, or for tidier directory listings in a subdirectory called ".embossdata". Files for all EMBOSS runs can be put in the user's home directory, or again in a subdirectory called ".embossdata".

The directories are searched in the following order:

.	your current directory
.embossdata/	under your current directory
~/	your home directory
~/.embossdata/	under your home directory

Notes

Where the two sequences have substantial regions of similarity, the dots line up to form diagonal lines. It is possible to see at a glance such local regions of similarity. It is also easy to see other features such as repeats (which form parallel diagonal lines), and insertions or deletions (which form breaks or discontinuities in the diagonal lines).

References

None.

Warnings

None.

Diagnostic Error Messages

None.

Exit status

It always exits with status 0.

Known bugs

None.

See also

dotpath	Draw a non-overlapping wordmatch dotplot of two sequences
dottup	Displays a wordmatch dotplot of two sequences
polydot	Draw dotplots for all-against-all comparison of a sequence set

<a href="dottup.html">dottup,</a> by comparison, has no threshold, using a wordmatch-style method. dottup is less sensitive, but substantially faster than dotmatcher.

Author(s)

Ian Longden formerly at Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK.

Please report all bugs to the EMBOSS bug team (emboss-bug (@) emboss.open-bio.org) not to the original author.

History

Completed 1st June 1999.

Target users

This program is intended to be used by everyone and everything, from naive users to embedded scripts.

Comments

None