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.
Count number of Serine/threonine/tyrosine residues in certain genes ?!
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
• 1,764 views
•
link
updated
by
Elisabeth Gasteiger
•
written
by
moustafa_abohawya •
•
written
by
moustafa_abohawya •
2 answers
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.
• 0 views
•
link
written
by
Elisabeth Gasteiger
Log in to answer this question.
More posts like this
-
Efetch from eutilities gives '400 Bad Request'; how to fix this?
written by Shraddha •
-
Add text to fasta header based in a list
written by cabraham03 •
-
Data Visualization tool for mutations difference between primary and metastatic tumor.
written by moustafa_abohawya •
-
Retrieve / Generate Naive PDB test structures for neighbor search algorithm (Biopython)
written by jonbroad15 •
-
Classic threshold for log2 fold change in RNA-seq experiment
written by Mozart
-
Negative Phosphosites Dataset Generation/Gathering
written by asdfxzsdf2 •
-
How to search Pfam DB using list of accessions
written by Medhat
-
Will the real kinases please stand up?
written by cdsouthan
-
In Rna-Seq Data, How To Separate Intronic, Exonic, Non-Coding, Snornas ?
written by newDNASeqer
-
Using Hmmer 3.0 To Search For Domains Containing A Ptm
written by aarstar •
