Program gto_amino_acid_from_seq

The gto_amino_acid_from_seq converts DNA sequence to an amino acid sequence.

For help type:

./gto_amino_acid_from_seq -h


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

Input parameters

The gto_amino_acid_from_seq program needs two streams for the computation, namely the input and output standard. The input stream is a DNA sequence.

The attribution is given according to:

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

It converts DNA sequence to an amino acid sequence (translation).


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

Basic options
< input.seq Input sequence file (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_seq < input.seq > output.prot


An example of such an input file is:

ACAAGACGGCCTCCTGCTGCTGCTGCTCTCCGGGGCCACGGCCCTGGAGGGTCCACCGCTGCCCTGCTGCCATTGTCCC
CGGCCCCACCTAAGGAAAAGCAGCCTCCTGACTTTCCTCGCTTGGGCCGAGACAGCGAGCATATGCAGGAAGCGGCAGG
AAGTGGTTTGAGTGGACCTCCGGGCCCCTCATAGGAGAGGAAGCTCGGGAGGTGGCCAGGCGGCAGGAAGCAGGCCAGT
GCCGCGAATCCGCGCGCCGGGACAGAATCTCCTGCAAAGCCCTGCAGGAACTTCTTCTGGAAGACCTTCTCCACCCCCC
CAGCTAAAACCTCACCCATGAATGCTCACGCAAGTTTAATTACAGACCTGAAACAAGATGCCATTGTCCCCCGGCCTCC
TGCTGCTGCTGCTCTCCGGGGCCACGGCCACCGCTGCCCTGCCCCTGGAGGGTGGCCCCACCGGCCGAGACAGCGAGCA
TATGCAGGAAGCGGCAGGAATAAGGAAAAGCAGCCTCCTGACTTTCCTCGCTTGGTGGTTTGAGTGGACCTCCCAGGCC
AGTGCCGGGCCCCTCATAGGAGAGGAAGCTCGGGAGGTGGCCAGGCGGCAGGAAGGCGCACCCCCCCAGCAATCCGCGC
GCCGGGACAGAATGCCCTGCAGGAACTTCTTCTGGAAGACCTTCTCCTCCTGCAAATAAAACCTCACCCATGAATGCTC
ACGCAAGTTTAATTACAGACCTGAA


Output

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

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

TRRPPAAAALRGHGPGGSTAALLPLSPAPPKEKQPPDFPRLGRDSEHMQEAAGSGLSGPPGPS-ERKLGRWPGGRKQAS
AANPRAGTESPAKPCRNFFWKTFSTPPAKTSPMNAHASLITDLKQDAIVPRPPAAAALRGHGHRCPAPGGWPHRPRQRA
YAGSGRNKEKQPPDFPRLVV-VDLPGQCRAPHRRGSSGGGQAAGRRTPPAIRAPGQNALQELLLEDLLLLQIKPHP-ML
TQV-LQT-