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

Iddo Friedberg idoerg at burnham.org
Fri Jul 22 12:38:40 EDT 2005


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


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.


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
10901 N. Torrey Pines Rd.
La Jolla, CA 92037 USA
Tel: +1 (858) 646 3100 x3516
Fax: +1 (858) 713 9949

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