| wordmatch

## Function

Finds all exact matches of a given size between 2 sequences

## Description

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]:
    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

       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)

## 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               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
    //

### Database entry: tsw:hbb_human

    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
    //

## 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: 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

    #---------------------------------------
    #---------------------------------------

### File: HBA_HUMAN.gff

    ##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"

### File: HBB_HUMAN.gff

    ##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.

## 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
wordfinder | Match large sequences against one or more other sequences

## Author(s)

Ian Longden (il © sanger.ac.uk)
Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK.

## History

Completed 27th November 1998.

## Target users

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

## Comments