NdPASA: a pairwise sequence alignment server for ...
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NdPASA: a pairwise sequence alignment server for ...
NdPASA: a pairwise sequence alignment server for distantly related proteins Wei Li1 , Junwen Wang2,† and Jin-An Feng1,2,∗ 1 Department
of Chemistry and 2 Center for Biotechnology, Temple University, Philadelphia, PA 19122, USA
Received on May 9, 2005; revised on July 13, 2005; accepted on August 8, 2005 Advance Access publication August 16, 2005
Protein sequence alignment is an essential component of biomedical research. It is one of the standard approaches to explore potential functional activity of a newly discovered protein by identifying sequence homologues that may be evolutionarily related (Pearson and Lipman, 1988). Structural and functional information of a new protein can often be inferred from the knowledge of wellcharacterized homologous proteins. An accurate sequence alignment is critical to comparative protein structure prediction. While closely related protein sequences in general are relatively easy to align using the existing sequence-based methods, the success rate of these methods in finding correct alignment is significantly reduced when the sequence identity between two aligned sequences is
