EMBOSS: Stretcher

Program Stretcher ( YMBC , NCHC )

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]           outfile    Output file name

   Optional qualifiers:
   -datafile           matrix     Matrix file
   -gappenalty         integer    gappenalty
   -gaplength          integer    gap length penalty
   -markx              integer    alternative displays
   -length             integer    number per line

   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)		 Output file name Output file <sequence>.stretcher
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
-markx alternative displays Positive integer up to 10 0
-length number per line Positive integer 60
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:

Notes

References

  1. Myers and Miller, CABIOS (1989)

Warnings

Diagnostic Error Messages

Exit status

Known bugs

See also

est2genomeAlign EST and genomic DNA sequences
needleNeedleman-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