SB Back translate - mendessoares/BuddySuite GitHub Wiki

--back_translate, -btr

Description

Convert an amino acid sequence to codons, selecting from a random codon distribution or from the distribution within a specific species. You can also choose to only use the most favorable (optimized) codon from a specified species.

Arguments

Species ( {human, h, mouse, m, yeast, y, ecoli, e} )

Optional. The relative codon frequency fluctuates among species. Use this argument to select a species-specific codon distribution (default=None).

Mode ( {random, r, optimal, o} )

Optional. Select 'optimal' to generate a deterministic dna sequence with only the most common (species specific) codon selected for each amino acid. Choosing 'random' will draw codons completely at random or from their species specific relative distribution if a species was selected (default=random).

Examples

Input file: ML25998a.fa

>ML25998a.
MVLDLISGSLNGFLKIKSVSIDDQWDQINRTYLVMFCILSGTIMTFKQNLGSIIHCISDA
RGDDSSFADAHATFVQDYCAAQGLYTLKEVYDKSWPDEIPYPGILQMKTIGCFPGRQFKN

Usage example 1

$: sb ML25998a.fa -btr

Output

>ML25998a.
ATGGTTCTCGACCTAATATCTGGCAGTTTAAATGGATTTTTGAAAATCAAGAGTGTTTCT
ATCGATGACCAGTGGGACCAAATTAATAGAACTTATCTAGTCATGTTTTGTATTCTAAGC
GGGACCATTATGACATTCAAACAAAATCTGGGGTCCATCATACATTGCATATCAGACGCA
CGCGGAGACGACTCGAGTTTCGCAGACGCTCATGCTACCTTCGTACAGGACTACTGTGCT
GCTCAGGGCCTCTACACACTGAAGGAAGTCTATGATAAAAGTTGGCCCGATGAGATACCC
TACCCAGGCATACTACAGATGAAAACAATAGGGTGTTTTCCAGGACGGCAGTTTAAAAAT

Usage example 2

$: sb ML25998a.fa -btr 'ecoli' 'random'

Output

>ML25998a.
ATGGTACTGGATCTTATCAGTGGGTCGTTGAATGGCTTCCTGAAAATTAAATCTGTGTCG
ATTGACGATCAATGGGATCAGATCAACCGTACATATTTAGTGATGTTCTGTATCCTGTCA
GGCACGATCATGACTTTTAAACAGAATCTGGGCAGCATAATTCACTGCATCAGCGATGCG
CGTGGGGATGATAGTTCGTTCGCCGATGCGCATGCCACATTCGTGCAAGACTATTGCGCA
GCTCAAGGCCTCTATACCCTAAAAGAGGTTTATGATAAGTCGTGGCCCGATGAGATTCCG
TACCCGGGCATCTTGCAGATGAAAACCATTGGCTGCTTTCCTGGTCGACAGTTTAAAAAT

Usage example 3

$: sb ML25998a.fa -btr 'o' 'h'

Output

>ML25998a.
ATGGTGCTGGACCTGATCAGCGGCAGCCTGAACGGCTTCCTGAAGATCAAGAGCGTGAGC
ATCGACGACCAGTGGGACCAGATCAACAGAACCTACCTGGTGATGTTCTGCATCCTGAGC
GGCACCATCATGACCTTCAAGCAGAACCTGGGCAGCATCATCCACTGCATCAGCGACGCC
AGAGGCGACGACAGCAGCTTCGCCGACGCCCACGCCACCTTCGTGCAGGACTACTGCGCC
GCCCAGGGCCTGTACACCCTGAAGGAGGTGTACGACAAGAGCTGGCCCGACGAGATCCCC
TACCCCGGCATCCTGCAGATGAAGACCATCGGCTGCTTCCCCGGCAGACAGTTCAAGAAC