Tehdyt toimenpiteet
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wordmatch |
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Function
Finds regions of identity (exact matches) of two sequencesDescription
wordmatch finds all regions of identity (exact matches) of a specified minimum size of two input sequences. These regions are reported in a standard EMBOSS alignment file and in standard EMBOSS sequence feature files.
Usage
Here is a sample session with wordmatch
% wordmatch tsw:hba_human tsw:hbb_human Finds regions of identity (exact matches) of two sequences Word size [4]: Output alignment [hba_human.wordmatch]: Features output [HBA_HUMAN.gff]: Second features output [HBB_HUMAN.gff]: |
Go to the input files for this example
Go to the output files for this example
Command line arguments
Finds regions of identity (exact matches) of two sequences
Version: EMBOSS:6.4.0.0
Standard (Mandatory) qualifiers:
[-asequence] seqset Sequence set filename and optional format,
or reference (input USA)
[-bsequence] seqall Sequence(s) filename and optional format, or
reference (input USA)
-wordsize integer [4] Word size (Integer 2 or more)
[-outfile] align [*.wordmatch] Output alignment file name
(default -aformat match)
[-aoutfeat] featout [unknown.gff] Output features UFO
[-boutfeat] featout [unknown.gff] Output features UFO
Additional (Optional) qualifiers:
-[no]dumpalign toggle [Y] Dump matches as alignments
-logfile outfile [wordmatch.log] Statistics on distribution
of kmers and matches
-[no]dumpfeat toggle [Y] Dump matches as feature files
Advanced (Unprompted) qualifiers: (none)
Associated qualifiers:
"-asequence" associated qualifiers
-sbegin1 integer Start of each sequence to be used
-send1 integer End of each 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 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
"-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
"-logfile" associated qualifiers
-odirectory string Output directory
"-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 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 |
|---|---|---|---|---|
| Standard (Mandatory) qualifiers | ||||
| [-asequence] (Parameter 1) |
seqset | Sequence set filename and optional format, or reference (input USA) | Readable set of sequences | Required |
| [-bsequence] (Parameter 2) |
seqall | Sequence(s) filename and optional format, or reference (input USA) | Readable sequence(s) | Required |
| -wordsize | integer | Word size | Integer 2 or more | 4 |
| [-outfile] (Parameter 3) |
align | Output alignment file name | (default -aformat match) | <*>.wordmatch |
| [-aoutfeat] (Parameter 4) |
featout | Output features UFO | Writeable feature table | unknown.gff |
| [-boutfeat] (Parameter 5) |
featout | Output features UFO | Writeable feature table | unknown.gff |
| Additional (Optional) qualifiers | ||||
| -[no]dumpalign | toggle | Dump matches as alignments | Toggle value Yes/No | Yes |
| -logfile | outfile | Statistics on distribution of kmers and matches | Output file | wordmatch.log |
| -[no]dumpfeat | toggle | Dump matches as feature files | Toggle value Yes/No | Yes |
| Advanced (Unprompted) qualifiers | ||||
| (none) | ||||
| Associated qualifiers | ||||
| "-asequence" associated seqset qualifiers | ||||
| -sbegin1 -sbegin_asequence |
integer | Start of each sequence to be used | Any integer value | 0 |
| -send1 -send_asequence |
integer | End of each 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 seqall qualifiers | ||||
| -sbegin2 -sbegin_bsequence |
integer | Start of each sequence to be used | Any integer value | 0 |
| -send2 -send_bsequence |
integer | End of each 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 | |
| "-outfile" associated align qualifiers | ||||
| -aformat3 -aformat_outfile |
string | Alignment format | Any string | match |
| -aextension3 -aextension_outfile |
string | File name extension | Any string | |
| -adirectory3 -adirectory_outfile |
string | Output directory | Any string | |
| -aname3 -aname_outfile |
string | Base file name | Any string | |
| -awidth3 -awidth_outfile |
integer | Alignment width | Any integer value | 0 |
| -aaccshow3 -aaccshow_outfile |
boolean | Show accession number in the header | Boolean value Yes/No | N |
| -adesshow3 -adesshow_outfile |
boolean | Show description in the header | Boolean value Yes/No | N |
| -ausashow3 -ausashow_outfile |
boolean | Show the full USA in the alignment | Boolean value Yes/No | N |
| -aglobal3 -aglobal_outfile |
boolean | Show the full sequence in alignment | Boolean value Yes/No | N |
| "-logfile" associated outfile qualifiers | ||||
| -odirectory | string | Output directory | Any string | |
| "-aoutfeat" associated featout qualifiers | ||||
| -offormat4 -offormat_aoutfeat |
string | Output feature format | Any string | gff |
| -ofopenfile4 -ofopenfile_aoutfeat |
string | Features file name | Any string | |
| -ofextension4 -ofextension_aoutfeat |
string | File name extension | Any string | |
| -ofdirectory4 -ofdirectory_aoutfeat |
string | Output directory | Any string | |
| -ofname4 -ofname_aoutfeat |
string | Base file name | Any string | $(asequence.name) |
| -ofsingle4 -ofsingle_aoutfeat |
boolean | Separate file for each entry | Boolean value Yes/No | N |
| "-boutfeat" associated featout qualifiers | ||||
| -offormat5 -offormat_boutfeat |
string | Output feature format | Any string | gff |
| -ofopenfile5 -ofopenfile_boutfeat |
string | Features file name | Any string | |
| -ofextension5 -ofextension_boutfeat |
string | File name extension | Any string | |
| -ofdirectory5 -ofdirectory_boutfeat |
string | Output directory | Any string | |
| -ofname5 -ofname_boutfeat |
string | Base file name | Any string | $(bsequence.name) |
| -ofsingle5 -ofsingle_boutfeat |
boolean | Separate file for each entry | Boolean value Yes/No | N |
| 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 |
Input file format
wordmatch reads two sets of nucleotide or protein sequences.
The input is a standard EMBOSS sequence query (also known as a 'USA').
Major sequence database sources defined as standard in EMBOSS installations include srs:embl, srs:uniprot and ensembl
Data can also be read from sequence output in any supported format written by an EMBOSS or third-party application.
The input format can be specified by using the command-line qualifier -sformat xxx, where 'xxx' is replaced by the name of the required format. The available format names are: gff (gff3), gff2, embl (em), genbank (gb, refseq), ddbj, refseqp, pir (nbrf), swissprot (swiss, sw), dasgff and debug.
See: http://emboss.sf.net/docs/themes/SequenceFormats.html for further information on sequence formats.
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 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 15-JUN-2010, entry version 86.
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
//
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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 15-JUN-2010, entry version 88.
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
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: multiple, simple, fasta, msf, clustal, mega, meganon, nexus,, nexusnon, phylip, phylipnon, selex, treecon, tcoffee, debug, srs.
The available pairwise alignment format names are: pair, markx0, markx1, markx2, markx3, markx10, match, sam, bam, score, srspair
See: http://emboss.sf.net/docs/themes/AlignFormats.html for further information on alignment formats.
By default the output is in 'match' format.
The matches in each set of input sequences are written as feature files.
The output is a standard EMBOSS feature file.
The results can be output in one of several styles by using the command-line qualifier -offormat xxx, where 'xxx' is replaced by the name of the required format. The available format names are: gff (gff3), gff2, embl (em), genbank (gb, refseq), ddbj, refseqp, pir (nbrf), swissprot (swiss, sw), dasgff and debug.
See: http://emboss.sf.net/docs/themes/FeatureFormats.html for further information on feature formats.
Output files for usage example
File: hba_human.wordmatch
########################################
# Program: wordmatch
# Rundate: Fri 15 Jul 2011 12:00:00
# Commandline: wordmatch
# [-asequence] tsw:hba_human
# [-bsequence] tsw:hbb_human
# Align_format: match
# Report_file: hba_human.wordmatch
########################################
#=======================================
#
# Aligned_sequences: 2
# 1: HBA_HUMAN
# 2: HBB_HUMAN
#=======================================
4 HBA_HUMAN + 15..18 HBB_HUMAN + 16..19
5 HBA_HUMAN + 59..63 HBB_HUMAN + 64..68
4 HBA_HUMAN + 117..120 HBB_HUMAN + 122..125
#---------------------------------------
#---------------------------------------
|
File: HBA_HUMAN.gff
##gff-version 3 ##sequence-region HBA_HUMAN 1 142 #!Date 2011-07-15 #!Type Protein #!Source-version EMBOSS 6.4.0.0 HBA_HUMAN wordmatch polypeptide_region 15 18 1.000 + . ID=HBA_HUMAN.1;note=HBB_HUMAN HBA_HUMAN wordmatch polypeptide_region 59 63 1.000 + . ID=HBA_HUMAN.2;note=HBB_HUMAN HBA_HUMAN wordmatch polypeptide_region 117 120 1.000 + . ID=HBA_HUMAN.3;note=HBB_HUMAN |
File: HBB_HUMAN.gff
##gff-version 3 ##sequence-region HBB_HUMAN 1 147 #!Date 2011-07-15 #!Type Protein #!Source-version EMBOSS 6.4.0.0 HBB_HUMAN wordmatch polypeptide_region 16 19 1.000 + . ID=HBB_HUMAN.1;note=HBA_HUMAN HBB_HUMAN wordmatch polypeptide_region 64 68 1.000 + . ID=HBB_HUMAN.2;note=HBA_HUMAN HBB_HUMAN wordmatch polypeptide_region 122 125 1.000 + . ID=HBB_HUMAN.3;note=HBA_HUMAN |
File: wordmatch.log
Small sequence/file for constructing target patterns: tsw:hba_human Large sequence/file to be scanned for patterns: tsw:hbb_human Number of sequences in the patterns file: 1 Pattern/word length: 4 Number of patterns/words found: 139 Number of sequences in the file scanned for patterns: 1 Number of all matches: 3 (wordmatch finds exact matches only) Sum of match lengths: 13 Average match length: 4.33 Distribution of the matches among pattern sequences: ---------------------------------------------------- HBA_HUMAN : 3 Pattern statistics: ------------------- Pattern #pat-sequences #all-matches avg-match-length EFTP : 1 1 4.00 HGKK : 1 1 5.00 WGKV : 1 1 4.00 |
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
wordmatch will only report identical regions that are at least as long as the specified wordsize.
References
None.Warnings
None.Diagnostic Error Messages
None.Exit status
0 if successful.Known bugs
None.See also
| Program name | Description |
|---|---|
| matcher | Waterman-Eggert local alignment of two sequences |
| seqmatchall | All-against-all word comparison of a sequence set |
| supermatcher | Calculate approximate local pair-wise alignments of larger sequences |
| water | Smith-Waterman local alignment of sequences |
| wordfinder | Match large sequences against one or more other sequences |
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.