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EMBOSS: backtranseq |
% backtranseq Back translate a protein sequence Input sequence: sw:opsd_human Output sequence [opsd_human.fasta]:
Here is a session using a drosophila sequence and codon table:
% backtranseq -cfile Edrosophila.cut Back translate a protein sequence Input sequence: sw:ach2_drome Output sequence [ach2_drome.fasta]:
Mandatory qualifiers: [-sequence] sequence Sequence USA [-outfile] seqout Output sequence USA Optional qualifiers: -cfile codon Codon usage table name 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 | |
---|---|---|---|
[-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) |
The output from the backtranslation of the human protein sw:opsd_human follows:
% more opsd_human.fasta >OPSD_HUMAN P08100 RHODOPSIN. ATGAACGGCACCGAGGGCCCCAACTTCTACGTGCCCTTCAGCAACGCCACCGGCGTGGTG AGAAGCCCCTTCGAGTACCCCCAGTACTACCTGGCCGAGCCCTGGCAGTTCAGCATGCTG GCCGCCTACATGTTCCTGCTGATCGTGCTGGGCTTCCCCATCAACTTCCTGACCCTGTAC GTGACCGTGCAGCACAAGAAGCTGAGAACCCCCCTGAACTACATCCTGCTGAACCTGGCC GTGGCCGACCTGTTCATGGTGCTGGGCGGCTTCACCAGCACCCTGTACACCAGCCTGCAC GGCTACTTCGTGTTCGGCCCCACCGGCTGCAACCTGGAGGGCTTCTTCGCCACCCTGGGC GGCGAGATCGCCCTGTGGAGCCTGGTGGTGCTGGCCATCGAGAGATACGTGGTGGTGTGC AAGCCCATGAGCAACTTCAGATTCGGCGAGAACCACGCCATCATGGGCGTGGCCTTCACC TGGGTGATGGCCCTGGCCTGCGCCGCCCCCCCCCTGGCCGGCTGGAGCAGATACATCCCC GAGGGCCTGCAGTGCAGCTGCGGCATCGACTACTACACCCTGAAGCCCGAGGTGAACAAC GAGAGCTTCGTGATCTACATGTTCGTGGTGCACTTCACCATCCCCATGATCATCATCTTC TTCTGCTACGGCCAGCTGGTGTTCACCGTGAAGGAGGCCGCCGCCCAGCAGCAGGAGAGC GCCACCACCCAGAAGGCCGAGAAGGAGGTGACCAGAATGGTGATCATCATGGTGATCGCC TTCCTGATCTGCTGGGTGCCCTACGCCAGCGTGGCCTTCTACATCTTCACCCACCAGGGC AGCAACTTCGGCCCCATCTTCATGACCATCCCCGCCTTCTTCGCCAAGAGCGCCGCCATC TACAACCCCGTGATCTACATCATGATGAACAAGCAGTTCAGAAACTGCATGCTGACCACC ATCTGCTGCGGCAAGAACCCCCTGGGCGACGACGAGGCCAGCGCCACCGTGAGCAAGACC GAGACCAGCCAGGTGGCCCCCGCC
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 |
---|---|
charge | Protein charge plot |
checktrans | Reports STOP codons and ORF statistics of a protein sequence |
coderet | Extract CDS, mRNA and translations from feature tables |
compseq | Counts the composition of dimer/trimer/etc words in a sequence |
emowse | Protein identification by mass spectrometry |
iep | Calculates the isoelectric point of a protein |
mwfilter | Filter noisy molwts from mass spec output |
octanol | Displays protein hydropathy |
pepinfo | Plots simple amino acid properties in parallel |
pepstats | Protein statistics |
pepwindow | Displays protein hydropathy |
pepwindowall | Displays protein hydropathy of a set of sequences |
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 |