[BiO BB] Re: BiO_Bulletin_Board Digest, Vol 28, Issue 4

[Carlos Manuel Estevez-Breton]

bio_bulletin_board-request at bioinformatics.org escribió:
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> Today's Topics:
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>    1. how to identify the function and structure of a novel
>       sequence (Li Xue)
>    2. CFP: SPAC 07 - Software Patterns: Addressing Challenges
>       (eduardo segura)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Fri, 02 Feb 2007 16:04:45 -0600
> From: Li Xue <lixue at iastate.edu>
> Subject: [BiO BB] how to identify the function and structure of a
> 	novel	sequence
> To: bio_bulletin_board at bioinformatics.org
> Message-ID: <200702022204.l12M4k8p027478 at mailhub-3.iastate.edu>
> Content-Type: text/plain; charset="us-ascii"; format=flowed
>
> hello all,
>
> I have a novel sequence(the protein sequence, DNA sequence, the 
> coding sequence, and the cDNA sequence).
>
> I tried BLASTn, BLASTx, and PSI-BLAST with default parameters and 
> modified parameters which loosed the restriction to try to find 
> distantly related matches. What I got are only unknown sequences and 
> hypothetical sequences.
>
> I also tried EBI Interpro with default parameters. No hits.
>
> Can someone offer some ways to identify the function and the 
> structure of  a new sequence? Thank you.
>
> Li
>   
Li,

Have you tried with structural motifs, bolcks or domains.

The method thad we use is search well known structures, mach them and 
then simulate the no well residues.

-- 
_____________________________________
Carlos Manuel Estevez-Breton R. MSc.
Coordinador Unidad de Sistemas
Facultad de Ciencias
Pontificia Universidad Javeriana
Tel (+571) 320 8320 Ext. 4033/32
Av7 No. 40-62 Bogota D.C.
Colombia


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