
                             EMBOSS: Stretcher
     _________________________________________________________________
   
                               Program Stretcher
                                       
Function

   Finds the best global alignment between two sequences
   
Description


 calculates a global alignment of two sequences

 Please cite: Myers and Miller, CABIOS (1989)
 version 2.0u. Modified for EMBOSS May 1999

Usage

   Here is a sample session with stretcher.

 stretcher -sequencea s1 -sequenceb s2


 hbahum                                              141  vs.
 hbbhum                                              146
 scoring matrix: BLOSUM62, gap penalties: 12/2
 43.2% identity;         Global alignment score: 272

                 10        20        30        40         50
 hbahum V-LSPADKTNVKAAWGKVGAHAGEYGAEALERMFLSFPTTKTYFPHF-DLSH-----GSA
        : :.: .:. : : ::::  .. : :.::: :... .: :. .:  : :::      :.
 hbbhum VHLTPEEKSAVTALWGKV--NVDEVGGEALGRLLVVYPWTQRFFESFGDLSTPDAVMGNP
                10          20        30        40        50

             60        70        80        90       100       110
 hbahum QVKGHGKKVADALTNAVAHVDDMPNALSALSDLHAHKLRVDPVNFKLLSHCLLVTLAAHL
        .::.:::::  :.....::.:.. .....::.::. ::.::: ::.::.. :. .:: :.
 hbbhum KVKAHGKKVLGAFSDGLAHLDNLKGTFATLSELHCDKLHVDPENFRLLGNVLVCVLAHHF
        60        70        80        90       100       110

            120       130       140
 hbahum PAEFTPAVHASLDKFLASVSTVLTSKYR
          :::: :.:. .: .:.:...:. ::.
 hbbhum GKEFTPPVQAAYQKVVAGVANALAHKYH
       120       130       140

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
   -gappenalty         integer    gappenalty
   -gaplength          integer    gap length penalty

   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
   -gappenalty gappenalty Positive integer 12 for protein, 16 for nucleic
   -gaplength gap length penalty Positive integer 2 for protein, 4 for
   nucleic
   Advanced qualifiers Allowed values Default
   (none)
   
Input file format

   Any 2 sequence USAs of the same type (DNA or protein).
   
Output file format

Data files

   For protein sequences EBLOSUM62 is used for the substitution matrix.
   For nucleotide sequence, EDNAMAT is used. Others can be specified.
   
   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

References

    1. Myers and Miller, CABIOS (1989)
       
Warnings

Diagnostic Error Messages

Exit status

Known bugs

See also

   Program name                  Description
   alignwrap    Aligns a set of sequences to a seed alignment
   est2genome   Align EST and genomic DNA sequences
   needle       Needleman-Wunsch global alignment
   
Author(s)

   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 13th May 1999.

Target users

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