Program gto_amino_acid_from_fasta

The gto_amino_acid_from_fasta converts DNA sequences in FASTA or Multi-FASTA file format to an amino acid sequence.

For help type:


			  			./gto_amino_acid_from_fasta -h

In the following subsections, we explain the input and output paramters.

Input parameters

The gto_amino_acid_from_fasta program needs two streams for the computation, namely the input and output standard. The input stream is a FASTA or Multi-FASTA file.

The attribution is given according to:


			  			Usage: ../../bin/gto_amino_acid_from_fasta [options] [[--] args]
or: ../../bin/gto_amino_acid_from_fasta [options]

It converts FASTA or Multi-FASTA file format to an amino acid sequence (translation).

-h, --help            Show this help message and exit

Basic options
< input.mfasta        Input FASTA or Multi-FASTA file format (stdin)
> output.prot         Output amino acid sequence file (stdout)

Optional
-f, --frame=     Translation codon frame (1, 2 or 3)

Example: ../../bin/gto_amino_acid_from_fasta < input.mfasta > output.prot

An example of such an input file is:


			  			>AB000264 |acc=AB000264|descr=Homo sapiens mRNA
ACAAGACGGCCTCCTGCTGCTGCTGCTCTCCGGGGCCACGGCCCTGGAGGGTCCACCGCTGCCCTGCTGCCATTGTCCC
CGGCCCCACCTAAGGAAAAGCAGCCTCCTGACTTTCCTCGCTTGGGCCGAGACAGCGAGCATATGCAGGAAGCGGCAGG
AAGTGGTTTGAGTGGACCTCCGGGCCCCTCATAGGAGAGGAAGCTCGGGAGGTGGCCAGGCGGCAGGAAGCAGGCCAGT
GCCGCGAATCCGCGCGCCGGGACAGAATCTCCTGCAAAGCCCTGCAGGAACTTCTTCTGGAAGACCTTCTCCACCCCCC
CAGCTAAAACCTCACCCATGAATGCTCACGCAAGTTTAATTACAGACCTGAA
>AB000263 |acc=AB000263|descr=Homo sapiens mRNA
ACAAGATGCCATTGTCCCCCGGCCTCCTGCTGCTGCTGCTCTCCGGGGCCACGGCCACCGCTGCCCTGCCCCTGGAGGG
TGGCCCCACCGGCCGAGACAGCGAGCATATGCAGGAAGCGGCAGGAATAAGGAAAAGCAGCCTCCTGACTTTCCTCGCT
TGGTGGTTTGAGTGGACCTCCCAGGCCAGTGCCGGGCCCCTCATAGGAGAGGAAGCTCGGGAGGTGGCCAGGCGGCAGG
AAGGCGCACCCCCCCAGCAATCCGCGCGCCGGGACAGAATGCCCTGCAGGAACTTCTTCTGGAAGACCTTCTCCTCCTG
CAAATAAAACCTCACCCATGAATGCTCACGCAAGTTTAATTACAGACCTGAA

Output

The output of the gto_amino_acid_from_fasta program is an amino acid sequence.

Using the input above, an output example for this is the following:


			  			TRRPPAAAALRGHGPGGSTAALLPLSPAPPKEKQPPDFPRLGRDSEHMQEAAGSGLSGPPGPS-ERKLGRWPGGRKQAS
AANPRAGTESPAKPCRNFFWKTFSTPPAKTSPMNAHASLITDLTRCHCPPASCCCCSPGPRPPLPCPWRVAPPAETASI
CRKRQE-GKAAS-LSSLGGLSGPPRPVPGPS-ERKLGRWPGGRKAHPPSNPRAGTECPAGTSSGRPSPPANKTSPMNAH
ASLITDL