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wordmatch |
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.
% 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]: 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
Standard (Mandatory) qualifiers:
[-asequence] sequence Sequence filename and optional format, or
reference (input USA)
[-bsequence] sequence Sequence filename and optional format, or
reference (input USA)
-wordsize integer [4] Word size (Integer 2 or more)
[-outfile] align [*.wordmatch] Output alignment file name
[-aoutfeat] featout [unknown.gff] Output features UFO
[-boutfeat] featout [unknown.gff] 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 dying program messages
|
| Standard (Mandatory) qualifiers | Allowed values | Default | |
|---|---|---|---|
| [-asequence] (Parameter 1) |
Sequence filename and optional format, or reference (input USA) | Readable sequence | Required |
| [-bsequence] (Parameter 2) |
Sequence filename and optional format, or reference (input USA) | Readable sequence | Required |
| -wordsize | Word size | Integer 2 or more | 4 |
| [-outfile] (Parameter 3) |
Output alignment file name | Alignment output file | <*>.wordmatch |
| [-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) | |||
ID HBA_HUMAN Reviewed; 142 AA.
AC P69905; P01922; Q96KF1; Q9NYR7;
DT 21-JUL-1986, integrated into UniProtKB/Swiss-Prot.
DT 23-JAN-2007, sequence version 2.
DT 03-APR-2007, entry version 41.
DE Hemoglobin subunit alpha (Hemoglobin alpha chain) (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;
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;
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.";
RL Haematologica 86:541-542(2001).
RN [6]
[Part of this file has been deleted for brevity]
FT /FTId=VAR_002840.
FT VARIANT 131 131 A -> D (in Yuda; O(2) affinity down).
FT /FTId=VAR_002842.
FT VARIANT 131 131 A -> P (in Sun Prairie; unstable).
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 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; O(2) affinity 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 HELIX 4 15
FT HELIX 16 20
FT HELIX 21 35
FT HELIX 37 42
FT HELIX 53 71
FT HELIX 73 75
FT HELIX 76 79
FT HELIX 81 89
FT HELIX 96 112
FT TURN 114 116
FT HELIX 119 136
FT TURN 137 139
SQ SEQUENCE 142 AA; 15258 MW; 15E13666573BBBAE CRC64;
MVLSPADKTN VKAAWGKVGA HAGEYGAEAL ERMFLSFPTT KTYFPHFDLS HGSAQVKGHG
KKVADALTNA VAHVDDMPNA LSALSDLHAH KLRVDPVNFK LLSHCLLVTL AAHLPAEFTP
AVHASLDKFL ASVSTVLTSK YR
//
|
ID HBB_HUMAN Reviewed; 147 AA.
AC P68871; P02023; Q13852; Q14481; Q14510; Q45KT0; Q6FI08; Q8IZI1;
AC Q9BX96; Q9UCP8; Q9UCP9;
DT 21-JUL-1986, integrated into UniProtKB/Swiss-Prot.
DT 23-JAN-2007, sequence version 2.
DT 20-MAR-2007, entry version 43.
DE Hemoglobin subunit beta (Hemoglobin beta chain) (Beta-globin).
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.
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 [2]
RP NUCLEOTIDE SEQUENCE.
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 [3]
RP NUCLEOTIDE SEQUENCE.
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 [4]
RP NUCLEOTIDE SEQUENCE, AND VARIANT DURHAM-N.C. PRO-115.
RC TISSUE=Blood;
RA Kutlar F., Abboud M., Leithner C., Holley L., Brisco J., Kutlar A.;
RT "Electrophoretically silent, very unstable, thalassemic mutation at
RT codon 114 of beta globin (hemoglobin Durham-N.C.) detected by cDNA
RT sequencing of mRNA, from a Russian women.";
RL Submitted (AUG-1999) to the EMBL/GenBank/DDBJ databases.
RN [5]
RP NUCLEOTIDE SEQUENCE, AND VARIANT LOUISVILLE LEU-43.
RC TISSUE=Blood;
RA Kutlar F., Harbin J., Brisco J., Kutlar A.;
RT "Rapid detection of electrophoretically silent, unstable human
RT hemoglobin 'Louisville', (Beta; Phe 42 Leu/TTT to CTT) by cDNA
RT sequencing of mRNA.";
RL Submitted (JAN-1999) to the EMBL/GenBank/DDBJ databases.
RN [6]
RP NUCLEOTIDE SEQUENCE, AND VARIANT TY GARD GLN-125.
[Part of this file has been deleted for brevity]
FT VARIANT 141 141 A -> T (in St Jacques: O(2) affinity up).
FT /FTId=VAR_003081.
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 HELIX 5 15
FT TURN 20 22
FT HELIX 23 34
FT HELIX 36 41
FT HELIX 43 45
FT HELIX 51 56
FT HELIX 58 76
FT TURN 77 79
FT HELIX 81 93
FT TURN 94 96
FT HELIX 101 118
FT HELIX 119 121
FT HELIX 124 141
FT HELIX 143 145
SQ SEQUENCE 147 AA; 15998 MW; A31F6D621C6556A1 CRC64;
MVHLTPEEKS AVTALWGKVN VDEVGGEALG RLLVVYPWTQ RFFESFGDLS TPDAVMGNPK
VKAHGKKVLG AFSDGLAHLD NLKGTFATLS ELHCDKLHVD PENFRLLGNV LVCVLAHHFG
KEFTPPVQAA YQKVVAGVAN ALAHKYH
//
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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.
########################################
# Program: wordmatch
# Rundate: Sun 15 Jul 2007 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
#=======================================
5 HBA_HUMAN + 59..63 HBB_HUMAN + 64..68
4 HBA_HUMAN + 15..18 HBB_HUMAN + 16..19
4 HBA_HUMAN + 117..120 HBB_HUMAN + 122..125
#---------------------------------------
#---------------------------------------
|
##gff-version 2.0 ##date 2006-07-15 ##Type Protein HBA_HUMAN HBA_HUMAN wordmatch misc_feature 59 63 1.000 + . Sequence "HBA_HUMAN.1" ; note "HBB_HUMAN" HBA_HUMAN wordmatch misc_feature 15 18 1.000 + . Sequence "HBA_HUMAN.2" ; note "HBB_HUMAN" HBA_HUMAN wordmatch misc_feature 117 120 1.000 + . Sequence "HBA_HUMAN.3" ; note "HBB_HUMAN" |
##gff-version 2.0 ##date 2006-07-15 ##Type Protein HBB_HUMAN HBB_HUMAN wordmatch misc_feature 64 68 1.000 + . Sequence "HBB_HUMAN.1" ; note "HBA_HUMAN" HBB_HUMAN wordmatch misc_feature 16 19 1.000 + . Sequence "HBB_HUMAN.2" ; note "HBA_HUMAN" HBB_HUMAN wordmatch misc_feature 122 125 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.
| 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 |
| wordfinder | Match large sequences against one or more other sequences |