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stretcher |
calculates a global alignment of two sequences Please cite: Myers and Miller, CABIOS (1989) version 2.0u. Modified for EMBOSS May 1999
% stretcher tsw:hba_human tsw:hbb_human Finds the best global alignment between two sequences Output alignment [hba_human.stretcher]:
Mandatory qualifiers: [-sequencea] sequence Sequence USA [-sequenceb] sequence Sequence USA [-outfile] align Output alignment file name Optional qualifiers: -datafile matrix 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. -gappenalty integer Gap penalty -gaplength integer Gap length penalty Advanced qualifiers: (none) General qualifiers: -help boolean 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 alignment file name | Alignment file | |
Optional qualifiers | Allowed values | Default | |
-datafile | 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. | Comparison matrix file in EMBOSS data path | EBLOSUM62 for protein EDNAFULL for DNA |
-gappenalty | Gap penalty | 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) |
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: unknown, multiple, simple, fasta, msf, trace, srs
The available pairwise alignment format names are: pair, markx0, markx1, markx2, markx3, markx10, srspair, score
See: http://www.uk.embnet.org/Software/EMBOSS/Themes/AlignFormats.html for further information on alignment formats.
The output from the example follows:
######################################## # Program: stretcher # Rundate: Mon May 20 16:25:11 2002 # Report_file: hba_human.stretcher ######################################## #======================================= # # Aligned_sequences: 2 # 1: HBA_HUMAN # 2: HBB_HUMAN # Matrix: EBLOSUM62 # Gap_penalty: 12 # Extend_penalty: 2 # # Length: 148 # Identity: 64/148 (43.2%) # Similarity: 89/148 (60.1%) # Gaps: 9/148 ( 6.1%) # Score: 272 # # #======================================= 10 20 30 40 HBA_HU V-LSPADKTNVKAAWGKVGAHAGEYGAEALERMFLSFPTTKTYFPHF-DL : :.: .:. : : :::: .. : :.::: :... .: :. .: : :: HBB_HU VHLTPEEKSAVTALWGKV--NVDEVGGEALGRLLVVYPWTQRFFESFGDL 10 20 30 40 50 60 70 80 90 HBA_HU SH-----GSAQVKGHGKKVADALTNAVAHVDDMPNALSALSDLHAHKLRV : :. .::.::::: :.....::.:.. .....::.::. ::.: HBB_HU STPDAVMGNPKVKAHGKKVLGAFSDGLAHLDNLKGTFATLSELHCDKLHV 50 60 70 80 90 100 110 120 130 140 HBA_HU DPVNFKLLSHCLLVTLAAHLPAEFTPAVHASLDKFLASVSTVLTSKYR :: ::.::.. :. .:: :. :::: :.:. .: .:.:...:. ::. HBB_HU DPENFRLLGNVLVCVLAHHFGKEFTPPVQAAYQKVVAGVANALAHKYH 100 110 120 130 140 #--------------------------------------- #---------------------------------------
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:
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 |
Completed 13th May 1999.