[BiO BB] Re: pdb-l: Checking homology

[Iddo Friedberg]

Anshu,



If it is a sequence vs sequence comparison, then you can put the 
relevant subsequences into bl2seq, or any other pairwise sequence 
alignment program.

http://www.ncbi.nlm.nih.gov/blast/bl2seq/wblast2.cgi

If it is sequence vs. structure, i.e. modeling, then you can create a 
new PDB file by removing all the ATOM records from amino acids not in 
your subsequence.

./I






anshu verma wrote:

> Hi,
>  
> I have a protein. A portion of the protein forms a Beta barrel 
> structure. According to my literature serach, this particular portion 
> of the protein is analogous to a Beta barrel structure of  another 
> protein whose structure is known. I know BLAST can compare a 
> particular sequence to the known sequences/ structure in the data 
> bank. Is there any way of comparing a portion of the sequences of two 
> proteins? Eg. I want to take a particular portion of* protein A* and 
> compare it to a *particular portion* of *protein B* whose structure is 
> known, *but not the entire protein.*
> ** 
> Thanks,
> Anshu



-- 
Iddo Friedberg, Ph.D.
The Burnham Institute
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