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wordmatch |
Function
Finds all exact matches of a given size between 2 sequencesDescription
Finds all exact matches of a given minimum size between 2 sequences displaying the start points in each sequence and the match length.This program takes two sequences and finds regions where they are identical. These regions are reported in the output file (and optionally) in GFF (Gene Feature Format) files.
It will not find identical regions smaller than the specified wordsize.
Usage
Here is a sample session with wordmatch
% wordmatch tsw:hba_human tsw:hbb_human Finds all exact matches of a given size between 2 sequences Word size [4]: Output alignment [hba_human.wordmatch]: Output features [HBA_HUMAN.gff]: Second output features [HBB_HUMAN.gff]: |
Go to the input files for this example
Go to the output files for this example
Command line arguments
Standard (Mandatory) qualifiers:
[-asequence] sequence Sequence USA
[-bsequence] sequence Sequence USA
-wordsize integer Word size
[-outfile] align Output alignment file name
[-aoutfeat] featout Output features UFO
[-boutfeat] featout Output features UFO
Additional (Optional) qualifiers: (none)
Advanced (Unprompted) qualifiers: (none)
Associated qualifiers:
"-asequence" associated qualifiers
-sbegin1 integer Start of the sequence to be used
-send1 integer End of the sequence to be used
-sreverse1 boolean Reverse (if DNA)
-sask1 boolean Ask for begin/end/reverse
-snucleotide1 boolean Sequence is nucleotide
-sprotein1 boolean Sequence is protein
-slower1 boolean Make lower case
-supper1 boolean Make upper case
-sformat1 string Input sequence format
-sdbname1 string Database name
-sid1 string Entryname
-ufo1 string UFO features
-fformat1 string Features format
-fopenfile1 string Features file name
"-bsequence" associated qualifiers
-sbegin2 integer Start of the sequence to be used
-send2 integer End of the 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
"-outfile" associated qualifiers
-aformat3 string Alignment format
-aextension3 string File name extension
-adirectory3 string Output directory
-aname3 string Base file name
-awidth3 integer Alignment width
-aaccshow3 boolean Show accession number in the header
-adesshow3 boolean Show description in the header
-ausashow3 boolean Show the full USA in the alignment
-aglobal3 boolean Show the full sequence in alignment
"-aoutfeat" associated qualifiers
-offormat4 string Output feature format
-ofopenfile4 string Features file name
-ofextension4 string File name extension
-ofdirectory4 string Output directory
-ofname4 string Base file name
-ofsingle4 boolean Separate file for each entry
"-boutfeat" associated qualifiers
-offormat5 string Output feature format
-ofopenfile5 string Features file name
-ofextension5 string File name extension
-ofdirectory5 string Output directory
-ofname5 string Base file name
-ofsingle5 boolean Separate file for each entry
General qualifiers:
-auto boolean Turn off prompts
-stdout boolean Write standard output
-filter boolean Read standard input, write 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. 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 deaths
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| Standard (Mandatory) qualifiers | Allowed values | Default | |
|---|---|---|---|
| [-asequence] (Parameter 1) |
Sequence USA | Readable sequence | Required |
| [-bsequence] (Parameter 2) |
Sequence USA | Readable sequence | Required |
| -wordsize | Word size | Integer 2 or more | 4 |
| [-outfile] (Parameter 3) |
Output alignment file name | Alignment output file | |
| [-aoutfeat] (Parameter 4) |
Output features UFO | Writeable feature table | unknown.gff |
| [-boutfeat] (Parameter 5) |
Output features UFO | Writeable feature table | unknown.gff |
| Additional (Optional) qualifiers | Allowed values | Default | |
| (none) | |||
| Advanced (Unprompted) qualifiers | Allowed values | Default | |
| (none) | |||
Input file format
wordmatch reads any two sequence USAs of the same type (DNA or protein).Input files for usage example
'tsw:hba_human' is a sequence entry in the example protein database 'tsw'
Database entry: tsw:hba_human
ID HBA_HUMAN STANDARD; PRT; 141 AA.
AC P01922;
DT 21-JUL-1986 (Rel. 01, Created)
DT 21-JUL-1986 (Rel. 01, Last sequence update)
DT 15-JUL-1999 (Rel. 38, Last annotation update)
DE HEMOGLOBIN ALPHA CHAIN.
GN HBA1 AND HBA2.
OS Homo sapiens (Human), Pan troglodytes (Chimpanzee), and
OS Pan paniscus (Pygmy chimpanzee) (Bonobo).
OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Mammalia;
OC Eutheria; Primates; Catarrhini; Hominidae; Homo.
RN [1]
RP SEQUENCE FROM N.A. (ALPHA-1).
RX MEDLINE; 81088339.
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 SEQUENCE FROM N.A. (ALPHA-2).
RX MEDLINE; 81175088.
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 [3]
RP SEQUENCE FROM N.A. (ALPHA-2).
RX MEDLINE; 80137531.
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 [4]
RP SEQUENCE FROM N.A. (ALPHA-1 AND ALPHA-2).
RA FLINT J., HIGGS D.R.;
RL Submitted (JAN-1997) to the EMBL/GenBank/DDBJ databases.
RN [5]
RP SEQUENCE.
RA BRAUNITZER G., GEHRING-MULLER R., HILSCHMANN N., HILSE K., HOBOM G.,
RA RUDLOFF V., WITTMANN-LIEBOLD B.;
RT "The constitution of normal adult human haemoglobin.";
RL Hoppe-Seyler's Z. Physiol. Chem. 325:283-286(1961).
RN [6]
RP SEQUENCE.
RA HILL R.J., KONIGSBERG W.;
RT "The structure of human hemoglobin: IV. The chymotryptic digestion of
RT the alpha chain of human hemoglobin.";
RL J. Biol. Chem. 237:3151-3156(1962).
RN [7]
[Part of this file has been deleted for brevity]
FT /FTId=VAR_002841.
FT VARIANT 130 130 A -> D (IN YUDA; O2 AFFINITY DOWN).
FT /FTId=VAR_002842.
FT VARIANT 131 131 S -> P (IN QUESTEMBERT; HIGHLY UNSTABLE;
FT CAUSES ALPHA-THALASSEMIA).
FT /FTId=VAR_002843.
FT VARIANT 133 133 S -> R (IN VAL DE MARNE; O2 AFFINITY UP).
FT /FTId=VAR_002844.
FT VARIANT 135 135 V -> E (IN PAVIE).
FT /FTId=VAR_002845.
FT VARIANT 136 136 L -> M (IN CHICAGO).
FT /FTId=VAR_002846.
FT VARIANT 136 136 L -> P (IN BIBBA; UNSTABLE;
FT CAUSES ALPHA-THALASSEMIA).
FT /FTId=VAR_002847.
FT VARIANT 138 138 S -> P (IN ATTLEBORO; O2 AFFINITY UP).
FT /FTId=VAR_002848.
FT VARIANT 139 139 K -> E (IN HANAKAMI; O2 AFFINITY UP).
FT /FTId=VAR_002849.
FT VARIANT 139 139 K -> T (IN TOKONAME; O2 AFFINITY UP).
FT /FTId=VAR_002850.
FT VARIANT 140 140 Y -> H (IN ROUEN; O2 AFFINITY UP).
FT /FTId=VAR_002851.
FT VARIANT 141 141 R -> C (IN NUNOBIKI; O2 AFFINITY UP).
FT /FTId=VAR_002852.
FT VARIANT 141 141 R -> L (IN LEGNANO; O2 AFFINITY UP).
FT /FTId=VAR_002853.
FT VARIANT 141 141 R -> H (IN SURESNES; O2 AFFINITY UP).
FT /FTId=VAR_002854.
FT VARIANT 141 141 R -> P (IN SINGAPORE).
FT /FTId=VAR_002855.
FT HELIX 4 35
FT HELIX 37 42
FT TURN 44 45
FT TURN 50 51
FT HELIX 53 71
FT TURN 72 74
FT HELIX 76 79
FT TURN 80 80
FT HELIX 81 89
FT TURN 90 91
FT TURN 95 95
FT HELIX 96 112
FT TURN 114 116
FT HELIX 119 136
FT TURN 137 139
SQ SEQUENCE 141 AA; 15126 MW; 5EC7DB1E CRC32;
VLSPADKTNV KAAWGKVGAH AGEYGAEALE RMFLSFPTTK TYFPHFDLSH GSAQVKGHGK
KVADALTNAV AHVDDMPNAL SALSDLHAHK LRVDPVNFKL LSHCLLVTLA AHLPAEFTPA
VHASLDKFLA SVSTVLTSKY R
//
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Database entry: tsw:hbb_human
ID HBB_HUMAN STANDARD; PRT; 146 AA.
AC P02023;
DT 21-JUL-1986 (Rel. 01, Created)
DT 21-JUL-1986 (Rel. 01, Last sequence update)
DT 15-JUL-1999 (Rel. 38, Last annotation update)
DE HEMOGLOBIN BETA CHAIN.
GN HBB.
OS Homo sapiens (Human), Pan troglodytes (Chimpanzee), and
OS Pan paniscus (Pygmy chimpanzee) (Bonobo).
OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Mammalia;
OC Eutheria; Primates; Catarrhini; Hominidae; Homo.
RN [1]
RP SEQUENCE.
RC SPECIES=HUMAN;
RA BRAUNITZER G., GEHRING-MULLER R., HILSCHMANN N., HILSE K., HOBOM G.,
RA RUDLOFF V., WITTMANN-LIEBOLD B.;
RT "The constitution of normal adult human haemoglobin.";
RL Hoppe-Seyler's Z. Physiol. Chem. 325:283-286(1961).
RN [2]
RP SEQUENCE FROM N.A.
RC SPECIES=HUMAN;
RX MEDLINE; 81064667.
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 SEQUENCE OF 121-146 FROM N.A.
RC SPECIES=HUMAN;
RX MEDLINE; 85205333.
RA LANG K.M., SPRITZ R.A.;
RT "Cloning specific complete polyadenylylated 3'-terminal cDNA
RT segments.";
RL Gene 33:191-196(1985).
RN [4]
RP X-RAY CRYSTALLOGRAPHY (2.5 ANGSTROMS) OF DEOXYHEMOGLOBIN.
RC SPECIES=HUMAN;
RX MEDLINE; 76027820.
RA FERMI G.;
RT "Three-dimensional fourier synthesis of human deoxyhaemoglobin at
RT 2.5-A resolution: refinement of the atomic model.";
RL J. Mol. Biol. 97:237-256(1975).
RN [5]
RP SEQUENCE.
RC SPECIES=P.TROGLODYTES;
RX MEDLINE; 66071496.
RA RIFKIN D.B., KONIGSBERG W.;
RT "The characterization of the tryptic peptides from the hemoglobin of
RT the chimpanzee (Pan troglodytes).";
RL Biochim. Biophys. Acta 104:457-461(1965).
RN [6]
[Part of this file has been deleted for brevity]
FT VARIANT 140 140 A -> T (IN ST JACQUES: O2 AFFINITY UP).
FT /FTId=VAR_003081.
FT VARIANT 140 140 A -> V (IN PUTTELANGE; POLYCYTHEMIA;
FT O2 AFFINITY UP).
FT /FTId=VAR_003082.
FT VARIANT 141 141 L -> R (IN OLMSTED; UNSTABLE).
FT /FTId=VAR_003083.
FT VARIANT 142 142 A -> D (IN OHIO; O2 AFFINITY UP).
FT /FTId=VAR_003084.
FT VARIANT 143 143 H -> D (IN RANCHO MIRAGE).
FT /FTId=VAR_003085.
FT VARIANT 143 143 H -> Q (IN LITTLE ROCK; O2 AFFINITY UP).
FT /FTId=VAR_003086.
FT VARIANT 143 143 H -> P (IN SYRACUSE; O2 AFFINITY UP).
FT /FTId=VAR_003087.
FT VARIANT 143 143 H -> R (IN ABRUZZO; O2 AFFINITY UP).
FT /FTId=VAR_003088.
FT VARIANT 144 144 K -> E (IN MITO; O2 AFFINITY UP).
FT /FTId=VAR_003089.
FT VARIANT 145 145 Y -> C (IN RAINIER; O2 AFFINITY UP).
FT /FTId=VAR_003090.
FT VARIANT 145 145 Y -> H (IN BETHESDA; O2 AFFINITY UP).
FT /FTId=VAR_003091.
FT VARIANT 146 146 H -> D (IN HIROSHIMA; O2 AFFINITY UP).
FT /FTId=VAR_003092.
FT VARIANT 146 146 H -> L (IN COWTOWN; O2 AFFINITY UP).
FT /FTId=VAR_003093.
FT VARIANT 146 146 H -> P (IN YORK; O2 AFFINITY UP).
FT /FTId=VAR_003094.
FT VARIANT 146 146 H -> Q (IN KODAIRA; O2 AFFINITY UP).
FT /FTId=VAR_003095.
FT HELIX 5 15
FT TURN 16 17
FT HELIX 20 34
FT HELIX 36 41
FT HELIX 43 45
FT HELIX 51 55
FT TURN 56 56
FT HELIX 58 75
FT TURN 76 77
FT HELIX 78 94
FT TURN 95 96
FT TURN 100 100
FT HELIX 101 121
FT HELIX 124 142
FT TURN 143 144
SQ SEQUENCE 146 AA; 15867 MW; EC9744C9 CRC32;
VHLTPEEKSA VTALWGKVNV DEVGGEALGR LLVVYPWTQR FFESFGDLST PDAVMGNPKV
KAHGKKVLGA FSDGLAHLDN LKGTFATLSE LHCDKLHVDP ENFRLLGNVL VCVLAHHFGK
EFTPPVQAAY QKVVAGVANA LAHKYH
//
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Output file format
The output is a standard EMBOSS alignment file.
The results can be output in one of several styles by using the command-line qualifier -aformat xxx, where 'xxx' is replaced by the name of the required format. Some of the alignment formats can cope with an unlimited number of sequences, while others are only for pairs of sequences.
The available multiple alignment format names are: unknown, multiple, simple, fasta, msf, trace, srs
The available pairwise alignment format names are: pair, markx0, markx1, markx2, markx3, markx10, srspair, score
See: http://emboss.sf.net/docs/themes/AlignFormats.html for further information on alignment formats.
Output files for usage example
File: hba_human.wordmatch
########################################
# Program: wordmatch
# Rundate: Fri Jul 15 2005 12:00:00
# Align_format: match
# Report_file: hba_human.wordmatch
########################################
#=======================================
#
# Aligned_sequences: 2
# 1: HBA_HUMAN
# 2: HBB_HUMAN
#=======================================
5 HBA_HUMAN + 58..62 HBB_HUMAN + 63..67
4 HBA_HUMAN + 14..17 HBB_HUMAN + 15..18
4 HBA_HUMAN + 116..119 HBB_HUMAN + 121..124
#---------------------------------------
#---------------------------------------
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File: HBA_HUMAN.gff
##gff-version 2.0 ##date 2005-07-15 ##Type Protein HBA_HUMAN HBA_HUMAN wordmatch misc_feature 58 62 1.000 + . Sequence "HBA_HUMAN.1" ; note "HBB_HUMAN" HBA_HUMAN wordmatch misc_feature 14 17 1.000 + . Sequence "HBA_HUMAN.2" ; note "HBB_HUMAN" HBA_HUMAN wordmatch misc_feature 116 119 1.000 + . Sequence "HBA_HUMAN.3" ; note "HBB_HUMAN" |
File: HBB_HUMAN.gff
##gff-version 2.0 ##date 2005-07-15 ##Type Protein HBB_HUMAN HBB_HUMAN wordmatch misc_feature 63 67 1.000 + . Sequence "HBB_HUMAN.1" ; note "HBA_HUMAN" HBB_HUMAN wordmatch misc_feature 15 18 1.000 + . Sequence "HBB_HUMAN.2" ; note "HBA_HUMAN" HBB_HUMAN wordmatch misc_feature 121 124 1.000 + . Sequence "HBB_HUMAN.3" ; note "HBA_HUMAN" |
The normal 'report' header is output. It contains the details of the program run and the input sequences.
The data lines consist of five columns separated by spaces or TAB characters. Each line contains the information on one identical region. The first column is the length of the match. The second column is the name of the first sequence. The third column is the start and end position of the match. The next two columns are the name and positions of the second sequence.
Data files
None.Notes
None.References
None.Warnings
None.Diagnostic Error Messages
None.Exit status
0 if successful.Known bugs
None.See also
| Program name | Description |
|---|---|
| matcher | Finds the best local alignments between two sequences |
| seqmatchall | All-against-all comparison of a set of sequences |
| supermatcher | Match large sequences against one or more other sequences |
| water | Smith-Waterman local alignment |
Author(s)
Ian Longden (il © sanger.ac.uk)Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK.