[BiO BB] Re: BiO_Bulletin_Board Digest, Vol 20, Issue 5

Yannick Wurm Yannick.Wurm at unil.ch
Mon Jun 5 19:28:32 EDT 2006

Hi Daniel,

have a look at iprscan, which is a very complete tool:
For command-line access, see:
You can also set it up locally.

For each protein, the output is one line per domain found on that  
I concatenate the output files into one big file, and then count the  
different domains I have.


yannick.wurm at unil.ch  - Doctoral student
Department of Ecology and Evolution

#3106, Biophore, Universite de Lausanne
1015 Lausanne, Switzerland
land: +41.21.692.4182  fax: +41.21.692.4165
cell: +

On 5 juin 06, at 12:00, bio_bulletin_board-request at bioinformatics.org  

> I am after a way in which I can analyze large data sets of protein
> sequences, where the readout is a quantification of different protein
> domains that are found within a given list of sequences (e.g. a  
> list of
> 500 protein sequences in FASTA format).  Preferably the output  
> would be
> at the systems level (e.g. 230 Tyrosine Kinase domains) rather than  
> that
> describing domains only at a protein-by protein level.
> Thanks,
> Daniel

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