EMBOSS: Stretcher

Program Stretcher

Function

Description

 calculates a global alignment of two sequences

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

Usage

 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

Output file format

Data files

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

Author(s)

History

 Completed 13th May 1999.

Target users

Comments