## EMBOSS: matcher

# Program matcher

## Function

Finds the best local alignments between two sequences

## Description

matcher compares two sequences looking for local sequence similarities using a rigorous 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).

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

matcher will also report a specified number of alignments between the two sequences showing the actual local alignments. (water will only report the single best 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.

## Usage

Here is a sample session with matcher.

    % matcher sw:hba_human sw:hbb_human
    Finds the best local alignments between two sequences
    Output file [hba_human.matcher]:

Here is an example to find the 10 best alignments:

    % matcher sw:hba_human sw:hbb_human -alt 10
    Finds the best local alignments between two sequences
    Output file [hba_human.matcher]: hba_human.matcher10

## Command line arguments

       Mandatory qualifiers:
      [-sequencea]         sequence   Sequence USA
      [-sequenceb]         sequence   Sequence USA
      [-outfile]           align      (no help text) align value

       Optional qualifiers:
       -datafile           matrix     Matrix file
       -alternatives       integer    This sets the number of alternative matches
                                      output. By default only the highest scoring
                                      alignment is shown. A value of 2 gves you
                                      other reasonable alignments. In some cases,
                                      for example multidomain proteins of cDNA and
                                      gemomic DNA comparisons, there may be other
                                      interesting and significant alignments.
       -gappenalty         integer    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.
       -gaplength          integer    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.

       Advanced qualifiers: (none)
       General qualifiers:
      -help                bool       report command line options. More
                                      information on associated and general
                                      qualifiers can be found with -help -verbose

Mandatory qualifiers | Allowed values | Default
--- | --- | ---
[-sequencea] (Parameter 1) | Sequence USA | Readable sequence | Required
[-sequenceb] (Parameter 2) | Sequence USA | Readable sequence | Required
[-outfile] (Parameter 3) | (no help text) align value | Alignment file |
Optional qualifiers | Allowed values | Default
-datafile | Matrix file | Comparison matrix file in EMBOSS data path | EBLOSUM62 for protein EDNAFULL for DNA
-alternatives | This sets the number of alternative matches output. By default only the highest scoring alignment is shown. A value of 2 gves you other reasonable alignments. In some cases, for example multidomain proteins of cDNA and gemomic DNA comparisons, there may be other interesting and significant alignments. | Integer 1 or more | 1
-gappenalty | 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 | 14 for protein, 16 for nucleic

-gaplength

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

4 for any sequence

Advanced qualifiers | Allowed values | Default
(none)

## Input file format

Any 2 sequence USAs or the same type (DNA or protein).

## Output file format

The output from matcher is a sequence alignment.

Here is the output for the example:

      43.4% identity in 145 HBA_HUMAN overlap; score:  264

                  10        20        30        40         50
    HBA_HU LSPADKTNVKAAWGKVGAHAGEYGAEALERMFLSFPTTKTYFPHF-DLSH-----GSAQV
           :.: .:. : : ::::  .. : :.::: :... .: :. .:  : :::      :. .:
    HBB_HU LTPEEKSAVTALWGKV--NVDEVGGEALGRLLVVYPWTQRFFESFGDLSTPDAVMGNPKV
                 10          20        30        40        50        60

              60        70        80        90       100       110
    HBA_HU KGHGKKVADALTNAVAHVDDMPNALSALSDLHAHKLRVDPVNFKLLSHCLLVTLAAHLPA
           :.:::::  :.....::.:.. .....::.::. ::.::: ::.::.. :. .:: :.
    HBB_HU KAHGKKVLGAFSDGLAHLDNLKGTFATLSELHCDKLHVDPENFRLLGNVLVCVLAHHFGK
                   70        80        90       100       110       120

             120       130       140
    HBA_HU EFTPAVHASLDKFLASVSTVLTSKY
           :::: :.:. .: .:.:...:. ::
    HBB_HU EFTPPVQAAYQKVVAGVANALAHKY
                  130       140

    ----------

Here is the output for the example giving the 10 best alignments:

      43.4% identity in 145 HBA_HUMAN overlap; score:  264

                  10        20        30        40         50
    HBA_HU LSPADKTNVKAAWGKVGAHAGEYGAEALERMFLSFPTTKTYFPHF-DLSH-----GSAQV
           :.: .:. : : ::::  .. : :.::: :... .: :. .:  : :::      :. .:
    HBB_HU LTPEEKSAVTALWGKV--NVDEVGGEALGRLLVVYPWTQRFFESFGDLSTPDAVMGNPKV
                 10          20        30        40        50        60

              60        70        80        90       100       110
    HBA_HU KGHGKKVADALTNAVAHVDDMPNALSALSDLHAHKLRVDPVNFKLLSHCLLVTLAAHLPA
           :.:::::  :.....::.:.. .....::.::. ::.::: ::.::.. :. .:: :.
    HBB_HU KAHGKKVLGAFSDGLAHLDNLKGTFATLSELHCDKLHVDPENFRLLGNVLVCVLAHHFGK
                   70        80        90       100       110       120

             120       130       140
    HBA_HU EFTPAVHASLDKFLASVSTVLTSKY
           :::: :.:. .: .:.:...:. ::
    HBB_HU EFTPPVQAAYQKVVAGVANALAHKY
                  130       140

    ----------

      46.2% identity in 13 HBA_HUMAN overlap; score:   32

          60        70
    HBA_HU KKVADALTNAVAH
           .::. ...::.::
    HBB_HU QKVVAGVANALAH
                  140

    ----------

      38.9% identity in 18 HBA_HUMAN overlap; score:   28

          90       100
    HBA_HU KLRVDPVNFKLLSHCLLV
           :..:: :. . :.. :.:
    HBB_HU KVNVDEVGGEALGRLLVV
             20        30

    ----------

      60.0% identity in 10 HBA_HUMAN overlap; score:   23

          10
    HBA_HU VKAAWGKVGA
           :.::. :: :
    HBB_HU VQAAYQKVVA
             130

    ----------

      60.0% identity in 10 HBA_HUMAN overlap; score:   23

          80
    HBA_HU LSALSDLHAH
           :.:.::  ::
    HBB_HU LGAFSDGLAH
            70

    ----------

      29.4% identity in 17 HBA_HUMAN overlap; score:   21

             80        90
    HBA_HU PNALSALSDLHAHKLRV
           :.:. .   . ::  .:
    HBB_HU PDAVMGNPKVKAHGKKV
                   60

    ----------

      41.7% identity in 12 HBA_HUMAN overlap; score:   21

          30        40
    HBA_HU ERMFLSFPTTKT
           .:.: ::   .:
    HBB_HU QRFFESFGDLST
           40        50

    ----------

      50.0% identity in 8 HBA_HUMAN overlap; score:   20

              110
    HBA_HU LLVTLAAH
           .:: . ::
    HBB_HU VLVCVLAH
          110

    ----------

      50.0% identity in 12 HBA_HUMAN overlap; score:   20

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

    ----------

      28.6% identity in 21 HBA_HUMAN overlap; score:   19

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

    ----------

Here are the example outputs using other values of -markx:

    % matcher sw:hba_human sw:hbb_human stdout -markx 1
    Finds the best local alignments between two sequences

      43.4% identity in 145 HBA_HUMAN overlap; score:  264

                  10        20        30        40         50
    HBA_HU LSPADKTNVKAAWGKVGAHAGEYGAEALERMFLSFPTTKTYFPHF-DLSH-----GSAQV
            x Xx xX X X      xxX X x   X xxxXx X xXx XX     X      xXx
    HBB_HU LTPEEKSAVTALWGKV--NVDEVGGEALGRLLVVYPWTQRFFESFGDLSTPDAVMGNPKV
                 10          20        30        40        50        60

              60        70        80        90       100       110
    HBA_HU KGHGKKVADALTNAVAHVDDMPNALSALSDLHAHKLRVDPVNFKLLSHCLLVTLAAHLPA
            x     XX xxxxx  x xxXxxxxx  x  xX  x   X  x  xxX xXx  X xXX
    HBB_HU KAHGKKVLGAFSDGLAHLDNLKGTFATLSELHCDKLHVDPENFRLLGNVLVCVLAHHFGK
                   70        80        90       100       110       120

             120       130       140
    HBA_HU EFTPAVHASLDKFLASVSTVLTSKY
               X x xXx Xx x xxx xX
    HBB_HU EFTPPVQAAYQKVVAGVANALAHKY
                  130       140

    % matcher sw:hba_human sw:hbb_human stdout -markx 2
    Finds the best local alignments between two sequences

      43.4% identity in 145 HBA_HUMAN overlap; score:  264

                  10        20        30        40         50
    HBA_HU LSPADKTNVKAAWGKVGAHAGEYGAEALERMFLSFPTTKTYFPHF-DLSH-----GSAQV
    HBB_HU .T.EE.SA.T.L....--NVD.V.G...G.LLVVY.W.QRF.ES.G...TPDAVM.NPK.

              60        70        80        90       100       110
    HBA_HU KGHGKKVADALTNAVAHVDDMPNALSALSDLHAHKLRVDPVNFKLLSHCLLVTLAAHLPA
    HBB_HU .A.....LG.FSDGL..L.NLKGTFAT..E..CD..H...E..R..GNV.VCV..H.FGK

             120       130       140
    HBA_HU EFTPAVHASLDKFLASVSTVLTSKY
    HBB_HU ....P.Q.AYQ.VV.G.ANA.AH..

    % matcher sw:hba_human sw:hbb_human stdout -markx 3
    Finds the best local alignments between two sequences

      43.4% identity in 145 HBA_HUMAN overlap; score:  264
    >HBA_HUMAN ..
    LSPADKTNVKAAWGKVGAHAGEYGAEALERMFLSFPTTKTYFPHF-DLSH
    -----GSAQVKGHGKKVADALTNAVAHVDDMPNALSALSDLHAHKLRVDP
    VNFKLLSHCLLVTLAAHLPAEFTPAVHASLDKFLASVSTVLTSKY
    >HBB_HUMAN ..
    LTPEEKSAVTALWGKV--NVDEVGGEALGRLLVVYPWTQRFFESFGDLST
    PDAVMGNPKVKAHGKKVLGAFSDGLAHLDNLKGTFATLSELHCDKLHVDP
    ENFRLLGNVLVCVLAHHFGKEFTPPVQAAYQKVVAGVANALAHKY

    % matcher sw:hba_human sw:hbb_human stdout -markx 4
    Finds the best local alignments between two sequences

      43.4% identity in 145 HBA_HUMAN overlap; score:  264

    % matcher sw:hba_human sw:hbb_human stdout -markx 10
    Finds the best local alignments between two sequences
    >>#1
    ; sw_score: 264
    ; sw_ident: 0.434
    ; sw_overlap: 145
    >HBA_HUMAN ..
    ; sq_len: -115
    ; al_start: 2
    ; al_stop: 140
    ; al_display_start: 2
    LSPADKTNVKAAWGKVGAHAGEYGAEALERMFLSFPTTKTYFPHF-DLSH
    -----GSAQVKGHGKKVADALTNAVAHVDDMPNALSALSDLHAHKLRVDP
    VNFKLLSHCLLVTLAAHLPAEFTPAVHASLDKFLASVSTVLTSKY
    >HBB_HUMAN ..
    ; sq_len: 5
    ; al_start: 3
    ; al_stop: 145
    ; al_display_start: 3
    LTPEEKSAVTALWGKV--NVDEVGGEALGRLLVVYPWTQRFFESFGDLST
    PDAVMGNPKVKAHGKKVLGAFSDGLAHLDNLKGTFATLSELHCDKLHVDP
    ENFRLLGNVLVCVLAHHFGKEFTPPVQAAYQKVVAGVANALAHKY

Note that the parseable output starts each alignment record with ">>" while each aligned sequence record starts with ">".

All parameters produced will be of the form: ; xx_yyyyy

In this version, we have xx: sw - Smith-Waterman scores sq - sequence length, type al - alignment start, stop, display_offset

All of the output parameters correspond to values that are presented in other output formats, with the exception of the "al_" parameters.

al_start gives the location of the alignment start in the original sequence

al_stop gives the location of the end of the alignment in the original sequence

al_display_start gives the location of the first displayed amino acid residue in the original sequence. The -markx=10 alignments are the same as those produced in the other modes. If the beginning of the first sequence aligns with the 10'th residue of the second sequence, then the first sequence will be padded with ten leading "-" to produce the alignment. The leading '-' are a formatting convenience only; they are not considered in the numbering system for al_display_start, al_start, or al_stop.

## 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

None.

## 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 | Does an all-against-all comparison of a set of sequences
supermatcher | Finds a match of a large sequence against one or more sequences
water | Smith-Waterman local alignment
wordmatch | Finds all exact matches of a given size between 2 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 (il@sanger.ac.uk) Informatics Division, The Sanger Centre, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK.

## History

     Completed 11th May 1999.
     Last modified 19th July 1999.

## Target users

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

## Comments