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Whole Genome Amino Acid Composition Tool?

Hi there,

I'm interested in a statistical tool to get bacterial amino acid composition and genetic code usage at genome level.

I've looking in MESH terms database but I'm a bit lost. enter link description here

Thanks for your help. All the best, Bernardo

amino-acids codon bacteria
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updated by avkermanov • avkermanov • written by biotech biotech

2 answers

There is lots of software available to calculate amino acid composition and codon usage. Try searching with Google, not MeSH.

Couple of examples: the EMBOSS suite has lots of tools; here's a list for protein composition, here's another for nucleic codon usage.

Lots of R packages as well, e.g. seqinR.

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written by Neilfws Neilfws

It is a late answer, but for those, who is searching, and not able to write a python script, I can advice following: 1) from the NCBI genome (or any other source) download proteome file (all in fasta format); 2) download UGENE program, 3) open file in UGENE, choose option "merge sequence in 1", "set X to 0" when merging. 4) On the right bottom panel there will be histogram label - clicking on it you get statistics of all aminoacid in proteome in absolute and percentage values as table, copy-pastable to Excel. Good luck!

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written by avkermanov • avkermanov

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