[BiO BB] Domain Sequences

[Shameer Khadar]

Hi,

You have two option either you can download swissspfam from Pfam
ftp://ftp.sanger.ac.uk/pub/databases/Pfam/current_release/swisspfam.gz
or go to PRODOC - http://hodgkin.mbu.iisc.ernet.in/~prodoc/
and retreive domain assignments using the Pfam code.

Trust this help.

Shameer Khadar
Jr. Research Fellow
Prof. R. Sowdhamini's Lab (# 25) The Computational Biology Group
National Centre for Biological Sciences (TIFR)

On 11/10/06, Karthik Raman <karthik at rishi.serc.iisc.ernet.in> wrote:
>
> Hello
>
> I was just wondering if it is possible to download the domain details
> for individual proteins of an organism.
>
> It would be useful to have the domain details either in terms of the
> accession number and the span (start and end letters in the sequence)
> or better still as faa files giving individual domain sequence. Is it
> possible to retrieve this from databases such as Pfam or InterPro?
>
> Any pointers?
>
> Regards
> Karthik
>
> --
>
> **************************************************************************************
>    KARTHIK RAMAN
>    Graduate Research Student
>    Supercomputer Education and Research Centre/Bioinformatics Centre
>    Indian Institute of Science, Bangalore
>
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