                                  wordmatch



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Function

   Find regions of identity (exact matches) of two sequences

Description

   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
Find 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

Find regions of identity (exact matches) of two sequences
Version: EMBOSS:6.6.0.0

   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
   -scircular1         boolean    Sequence is circular
   -squick1            boolean    Read id and sequence only
   -sformat1           string     Input sequence format
   -iquery1            string     Input query fields or ID list
   -ioffset1           integer    Input start position offset
   -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
   -scircular2         boolean    Sequence is circular
   -squick2            boolean    Read id and sequence only
   -sformat2           string     Input sequence format
   -iquery2            string     Input query fields or ID list
   -ioffset2           integer    Input start position offset
   -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


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   13-JUN-2012, entry version 108.
DE   RecName: Full=Hemoglobin subunit alpha;
DE   AltName: Full=Alpha-globin;
DE   AltName: Full=Hemoglobin alpha chain;
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   13-JUN-2012, entry version 108.
DE   RecName: Full=Hemoglobin subunit beta;
DE   AltName: Full=Beta-globin;
DE   AltName: Full=Hemoglobin beta chain;
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: Mon 15 Jul 2013 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 2013-07-15
#!Type Protein
#!Source-version EMBOSS 6.6.0.0
HBA_HUMAN       wordmatch       polypeptide_region      15      18      1
.       .       ID=HBA_HUMAN.1;note=HBB_HUMAN
HBA_HUMAN       wordmatch       polypeptide_region      59      63      1
.       .       ID=HBA_HUMAN.2;note=HBB_HUMAN
HBA_HUMAN       wordmatch       polypeptide_region      117     120     1
.       .       ID=HBA_HUMAN.3;note=HBB_HUMAN

  File: HBB_HUMAN.gff

##gff-version 3
##sequence-region HBB_HUMAN 1 147
#!Date 2013-07-15
#!Type Protein
#!Source-version EMBOSS 6.6.0.0
HBB_HUMAN       wordmatch       polypeptide_region      16      19      1
.       .       ID=HBB_HUMAN.1;note=HBA_HUMAN
HBB_HUMAN       wordmatch       polypeptide_region      64      68      1
.       .       ID=HBB_HUMAN.2;note=HBA_HUMAN
HBB_HUMAN       wordmatch       polypeptide_region      122     125     1
.       .       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 (c) emboss.open-bio.org) not to the original author.

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

None
