                                   matcher



Wiki

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   http://emboss.open-bio.org/wiki/Appdocs on the EMBOSS Wiki.

   Please help by correcting and extending the Wiki pages.

Function

   Waterman-Eggert local alignment of two sequences

Description

   matcher identifies local similarities in two input sequences using a
   rigorous algorithm based on Bill Pearson's lalign application, version
   2.0u4 (Feb. 1996). The substitution matrix, gap insertion and extension
   penalty are specified. The specified number of top-scoring pair-wise
   local sequence alignments are written to file.

Algorithm

   matcher is based on Bill Pearson's lalign application, version 2.0u4
   (Feb. 1996). lalign uses code developed by X. Huang and W. Miller (Adv.
   Appl. Math. (1991) 12:337-357) for the "sim" program, which is a
   linear-space version of an algorithm described by M. S. Waterman and M.
   Eggert (J. Mol. Biol. 197:723-728).

Usage

   Here is a sample session with matcher


% matcher tsw:hba_human tsw:hbb_human
Waterman-Eggert local alignment of two sequences
Output alignment [hba_human.matcher]:


   Go to the input files for this example
   Go to the output files for this example

   Example 2

   To find the 10 best alignments:


% matcher tsw:hba_human tsw:hbb_human -alt 10
Waterman-Eggert local alignment of two sequences
Output alignment [hba_human.matcher]:


   Go to the output files for this example

Command line arguments

Waterman-Eggert local alignment of two sequences
Version: EMBOSS:6.6.0.0

   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)
  [-outfile]           align      [*.matcher] Output alignment file name
                                  (default -aformat markx0)

   Additional (Optional) qualifiers:
   -datafile           matrix     [EBLOSUM62 for protein, EDNAFULL for DNA]
                                  This is the scoring matrix file used when
                                  comparing sequences. By default it is the
                                  file 'EBLOSUM62' (for proteins) or the file
                                  'EDNAFULL' (for nucleic sequences). These
                                  files are found in the 'data' directory of
                                  the EMBOSS installation.
   -alternatives       integer    [1] This sets the number of alternative
                                  matches output. By default only the highest
                                  scoring alignment is shown. A value of 2
                                  gives you other reasonable alignments. In
                                  some cases, for example multidomain proteins
                                  of cDNA and genomic DNA comparisons, there
                                  may be other interesting and significant
                                  alignments. (Integer 1 or more)
   -gapopen            integer    [14 for protein, 16 for nucleic] The gap
                                  penalty is the score taken away when a gap
                                  is created. The best value depends on the
                                  choice of comparison matrix. The default
                                  value of 14 assumes you are using the
                                  EBLOSUM62 matrix for protein sequences, or a
                                  value of 16 and the EDNAFULL matrix for
                                  nucleotide sequences. (Positive integer)
   -gapextend          integer    [4 for any sequence] The gap length, or gap
                                  extension, penalty is added to the standard
                                  gap penalty for each base or residue in the
                                  gap. This is how long gaps are penalized.
                                  Usually you will expect a few long gaps
                                  rather than many short gaps, so the gap
                                  extension penalty should be lower than the
                                  gap penalty. An exception is where one or
                                  both sequences are single reads with
                                  possible sequencing errors in which case you
                                  would expect many single base gaps. You can
                                  get this result by setting the gap penalty
                                  to zero (or very low) and using the gap
                                  extension penalty to control gap scoring.
                                  (Positive integer)

   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
   -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 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
   -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

   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

   matcher reads in two 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.

  Output files for usage example

  File: hba_human.matcher

########################################
# Program: matcher
# Rundate: Mon 15 Jul 2013 12:00:00
# Commandline: matcher
#    [-asequence] tsw:hba_human
#    [-bsequence] tsw:hbb_human
# Align_format: markx0
# Report_file: hba_human.matcher
########################################

#=======================================
#
# Aligned_sequences: 2
# 1: HBA_HUMAN
# 2: HBB_HUMAN
# Matrix: EBLOSUM62
# Gap_penalty: 14
# Extend_penalty: 4
#
# Length: 145
# Identity:      63/145 (43.4%)
# Similarity:    88/145 (60.7%)
# Gaps:           8/145 ( 5.5%)
# Score: 264
#
#
#=======================================

             10        20        30        40         50
HBA_HU LSPADKTNVKAAWGKVGAHAGEYGAEALERMFLSFPTTKTYFPHF-DLSH
       :.: .:. : : ::::  .  : : ::: :. . .: :. .:  : :::
HBB_HU LTPEEKSAVTALWGKV--NVDEVGGEALGRLLVVYPWTQRFFESFGDLST
            10          20        30        40        50

                   60        70        80        90
HBA_HU -----GSAQVKGHGKKVADALTNAVAHVDDMPNALSALSDLHAHKLRVDP
            :. .:: :::::  : .. .::.:..    . ::.::  :: :::
HBB_HU PDAVMGNPKVKAHGKKVLGAFSDGLAHLDNLKGTFATLSELHCDKLHVDP
              60        70        80        90       100

        100       110       120       130       140
HBA_HU VNFKLLSHCLLVTLAAHLPAEFTPAVHASLDKFLASVSTVLTSKY
        ::.:: . :.  :: :   :::: : :.  : .: :.  :  ::
HBB_HU ENFRLLGNVLVCVLAHHFGKEFTPPVQAAYQKVVAGVANALAHKY
             110       120       130       140


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

  Output files for usage example 2

  File: hba_human.matcher

########################################
# Program: matcher
# Rundate: Mon 15 Jul 2013 12:00:00
# Commandline: matcher
#    [-asequence] tsw:hba_human
#    [-bsequence] tsw:hbb_human
#    -alternatives 10
# Align_format: markx0
# Report_file: hba_human.matcher
########################################

#=======================================
#
# Aligned_sequences: 2
# 1: HBA_HUMAN
# 2: HBB_HUMAN
# Matrix: EBLOSUM62
# Gap_penalty: 14
# Extend_penalty: 4
#
# Length: 145
# Identity:      63/145 (43.4%)
# Similarity:    88/145 (60.7%)
# Gaps:           8/145 ( 5.5%)
# Score: 264
#
#
#=======================================

             10        20        30        40         50
HBA_HU LSPADKTNVKAAWGKVGAHAGEYGAEALERMFLSFPTTKTYFPHF-DLSH
       :.: .:. : : ::::  .  : : ::: :. . .: :. .:  : :::
HBB_HU LTPEEKSAVTALWGKV--NVDEVGGEALGRLLVVYPWTQRFFESFGDLST
            10          20        30        40        50

                   60        70        80        90
HBA_HU -----GSAQVKGHGKKVADALTNAVAHVDDMPNALSALSDLHAHKLRVDP
            :. .:: :::::  : .. .::.:..    . ::.::  :: :::
HBB_HU PDAVMGNPKVKAHGKKVLGAFSDGLAHLDNLKGTFATLSELHCDKLHVDP
              60        70        80        90       100

        100       110       120       130       140
HBA_HU VNFKLLSHCLLVTLAAHLPAEFTPAVHASLDKFLASVSTVLTSKY
        ::.:: . :.  :: :   :::: : :.  : .: :.  :  ::
HBB_HU ENFRLLGNVLVCVLAHHFGKEFTPPVQAAYQKVVAGVANALAHKY
             110       120       130       140


#=======================================
#


  [Part of this file has been deleted for brevity]

#
# Aligned_sequences: 2
# 1: HBA_HUMAN
# 2: HBB_HUMAN
# Matrix: EBLOSUM62
# Gap_penalty: 14
# Extend_penalty: 4
#
# Length: 12
# Identity:       6/12 (50.0%)
# Similarity:     6/12 (50.0%)
# Gaps:           0/12 ( 0.0%)
# Score: 20
#
#
#=======================================

            120
HBA_HU HLPAEFTPAVHA
       ::  :   :: :
HBB_HU HLTPEEKSAVTA
             10


#=======================================
#
# Aligned_sequences: 2
# 1: HBA_HUMAN
# 2: HBB_HUMAN
# Matrix: EBLOSUM62
# Gap_penalty: 14
# Extend_penalty: 4
#
# Length: 21
# Identity:       6/21 (28.6%)
# Similarity:     7/21 (33.3%)
# Gaps:           0/21 ( 0.0%)
# Score: 19
#
#
#=======================================

           10        20
HBA_HU PADKTNVKAAWGKVGAHAGEY
       :      :   :   : : .:
HBB_HU PVQAAYQKVVAGVANALAHKY
         130       140


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

Data files

   For protein sequences EBLOSUM62 is used for the substitution matrix.
   For nucleotide sequence, EDNAFULL is used.

   EMBOSS data files are distributed with the application and stored in
   the standard EMBOSS data directory, which is defined by EMBOSS
   environment variable EMBOSS_DATA.

   Users can provide their own data files in their own directories.
   Project specific files can be put in the current directory, or for
   tidier directory listings in a subdirectory called ".embossdata". Files
   for all EMBOSS runs can be put in the user's home directory, or again
   in a subdirectory called ".embossdata".

   The directories are searched in the following order:
     * . (your current directory)
     * .embossdata (under your current directory)
     * ~/ (your home directory)
     * ~/.embossdata

Notes

   matcher is rigorous but also very slow. The advantage of matcher over
   water (which is also rigorous) is that it uses far less memory, so you
   are much less likely to run out of memory when aligning large
   sequences.

   matcher reports a specified number of alignments between the two
   sequences. water in contrast will only report only the single (optimal)
   match. The default number of alignments output is 1, but can be
   increased to (for example) the 10 best alignments by using the
   -alternatives 10 command-line qualifier. In some cases, for example
   multidomain proteins or cDNA and genomic DNA comparisons, there may be
   many interesting and significant alignments.

   matcher will not produce an alignment that is guaranteed to be optimal
   in the same way that water does, which implements the Needleman &
   Wunsch algorith. water will generate the single, optimal local
   alignment and uses memory in the order of the product of the lengths of
   the sequences to be aligned. If you require an optimal alignment you
   should use water. If you run out of memory or want several possible
   good alignments, use matcher.

References

    1. X. Huang and W. Miller (1991) Adv. Appl. Math. 12:373-381
    2. M. S. Waterman and M. Eggert (J. Mol. Biol. 197:723-728).

Warnings

   None.

Diagnostic Error Messages

   None.

Exit status

   0 upon successful completion.

Known bugs

   None.

See also

   Program name     Description
   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
   wordmatch        Find regions of identity (exact matches) of two sequences

   water will give a single best rigorous local alignment. It will use
   memory of the order of the product of the lengths of the sequences to
   be aligned. If you wish the 'best' local alignment you should use
   water. If you run out of memory or want several possible good
   alignments, use matcher.

Author(s)

   This program was originally written by Bill Pearson as part of the
   FASTA package under the name 'lalign'.

   This application was modified for inclusion in EMBOSS by 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 11th May 1999.

Target users

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

Comments

   None
