Count number of Serine/threonine/tyrosine residues in certain genes ?!

Question

[moustafa_abohawya]

I have a list of Arabidopsis Gene ID, I am interested to generate serine-threonine- tyrosine counts of residues in each one? Is there a way to do that for a large set of genes?

It is my first time to look for such aspect! I know the question may sound naive a bit!

Thanks in advance

Answer 1

[mastal511]

There are probably BioPerl or BioPython functions that will do this.

[DG]

I would use this approach. You can either download the genes of interest in FASTA format (or similar) or use a tool to automatically retrieve a sequence from NCBI (or another database) using the ID and calculate that. But BioPerl/Biopython both have sequence parsing methods that you can build on to do the counting.

Answer 2

[Elisabeth Gasteiger]

You could use ExPASy's ProtParam tool http://web.expasy.org/protparam which allows you to compute the amino acid composition for a given protein interactively.