Introduction

PeCoP stands for Persistently Conserved Positions. The PeCoP server offers a new way to examine positional conservation in protein sequences. The underlying rationale is that positions which are conserved in close and in distant sequence family members of the query sequence are more significant to the protein's structure and function than those simply conserved in close family members. Positions which are conserved in close family members may be conserved due to evolutionary non-divergence, and therefore may not have a role in the protein's structure or function. On the other hand, positions marked as conserved in distant family members may be marked as such due to errors in the multiple sequence alignment of remote sequences, which is tricky at best. The PeCoP server shows the conservation in varying degrees of family similarity to the query sequence, thus eliminating the false-positives that may be generated by alignments only to close and distant family members. It has been shown that this technique adds some 25% of information to the usual method of examining positional conservation in sequences, which is the "close-family" method.

Close and distant family members are collated using PSI-BLAST. Each iteration of PSI-BLAST creates a multiple sequence alignment and a profile (PSSM) by which the positional conservation is determined. Subsequent iterations of PSI-BLAST incorporate more distant sequences into the PSSM, thus refining the determination of conservation. The final output includes a consensus sequence, on which the persistently conserved positions are indicated. Final and interim results can also be emailed to the user. The emailed text files can be used to study the results.