[BiO BB] Re: BiO_Bulletin_Board digest, Vol 1 #601 - 3 msgs
dmb at mrc-dunn.cam.ac.uk
Fri Jan 9 04:26:45 EST 2004
++ sravan sravan--
> Hello everybody,
> I am working with secondary structure alignments. In
> order to optimize the gap penalties for the alignment of secondary structure
> strings with dynamic programming mehtod, I am using the following method.
> 1. Selecting of N number of pairs of proteins(each pair is a set of
> two structurally similar / sequence similarity: 70<%id<100) ).
> 2. secondary structure generation of the chains per pair.
> 3. Running the alignments of each pair with N combinations of gap
> penalties.(structure specific). 4. At wchich combination
> various proteins give highest structure alignment(sst aligns) with the paired one
> than with the others(low scores), that combination can be selected. queries:::
> 00) I am trying to select the similar pairs from FSSP table given by DALI.
> (TABLE2.html). In this pairs given in table I wanted to select the unique pairs
> based on a criteria (rmsd,%Id)..
> CAN I SELECT A PAIR WITH SEQ %ID: 70<%ID<100? WHAT
> SHOULD BE THE VALUE OF RMSD?
I would get all sequences in a fold then compare sequence identity, then pick pairs
from within the fold which match your criteria.
> (01) ANY IMPROVEMENTS TO THE METHOD I AM THINKING?
70% sequence identity is very high! -
> (01)ANY OTHER METHODLOGY TO OPTIMISE THE GAP PENALTIES FOR SECONDARY STRUCTURE
Probably many you could think of (i.e. counting the gaps between homologus pairs of
SS in structures), but none that I know of.
> Thank you all for the co operation.
> P.Sravana Kumar.
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