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EMBOSS: backtranseq |
% backtranseq Input sequence: sw:opsd_human Output sequence [opsd_human.fasta]:Here is a session using a drosophila sequence and codon table:
% backtranseq -seq sw:ach2_drome -out stdout -cfile Edrosophila
Mandatory qualifiers: [-sequence] sequence Sequence USA [-outfile] seqout Output sequence USA Optional qualifiers: -cfile codon Codon usage table name Advanced qualifiers: (none) |
Mandatory qualifiers | Allowed values | Default | |
---|---|---|---|
[-sequence] (Parameter 1) |
Sequence USA | Readable sequence | Required |
[-outfile] (Parameter 2) |
Output sequence USA | Writeable sequence | <sequence>.format |
Optional qualifiers | Allowed values | Default | |
-cfile | Codon usage table name | Codon usage file in EMBOSS data path | Ehum.cut |
Advanced qualifiers | Allowed values | Default | |
(none) |
To see the available EMBOSS codon usage files, run:
% embossdata -showall
To fetch one of the codon usage tables (for example 'Emus.cut') into your current directory for you to inspect or modify, run:
% embossdata -fetch -file Emus.cut
"The file 'drosoph.cut' does not exist" - the codon usage file cannot be opened.
Program name | Description |
---|---|
cusp | Create a codon usage table |
getorf | Finds and extracts open reading frames (ORFs) |
plotorf | Plot potential open reading frames |
prettyseq | Output sequence with translated ranges |
remap | Display a sequence with restriction cut sites, translation etc |
showorf | Pretty output of DNA translations |
showseq | Display a sequence with features, translation etc |
transeq | Translate nucleic acid sequences |