++ 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 > ALIGNMENT? 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. Cheers! > Regards. > P.Sravana Kumar. >