[BiO BB] how to identify the function and structure of a novelsequence

Martin Gollery marty.gollery at gmail.com
Mon Feb 5 12:12:23 EST 2007


Hi Li,

This comes up fairly regularly with new data. Even well studied
organisms have many sequences with unknown function. At some point,
you just have to get dirty and do a knockout or RNAi knockdown and see
what happens to the organism.

Marty

On 2/5/07, Li Xue <lixue at iastate.edu> wrote:
> 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
>
>
>
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-- 
-- 
Martin Gollery
Associate Director
Center For Bioinformatics
University of Nevada at Reno
Dept. of Biochemistry / MS334
775-784-7042
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