[BiO BB] Re: BiO_Bulletin_Board digest, Vol 1 #601 - 3 msgs

[sravan sravan]

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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:::
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 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?
 (01) ANY IMPROVEMENTS TO THE METHOD I AM THINKING?

 (01)ANY OTHER METHODLOGY TO OPTIMISE THE GAP PENALTIES FOR SECONDARY STRUCTURE ALIGNMENT?


Thank you all for the co operation.

Regards.
P.Sravana Kumar.