[BiO BB] Domain Prediction

[Boris Steipe]

If you want to compare your sequence against known domains, you can  
use RPS-Blast

    http://www.ncbi.nlm.nih.gov/Structure/cdd/wrpsb.cgi

or try a HMMER search against the SMART database

    http://smart.embl-heidelberg.de/smart/set_mode.cgi?NORMAL=1

HTH,

Boris



On 28 Apr 2006, at 05:09, Pooja Jain wrote:

> Hello everybody,
>
> I have sequenced a protein for which no structural signature can be  
> found in
> PDB.  I plan to identify domains in it. For this shall I BLAST it  
> against Pfam
> or some other database ? Ulternatively, can anyone suggest the most  
> accurate de
> novo or sequence similarity based domain prediction tool ?
>
> Thank you in advance.
>
> -Pooja
>
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