PAL: A Perl Script for Rapidly Identifying the Active Site of Large Protein Families

Abstract

In the post-genomic era, with an ever-increasing amount of sequence information, it is critical to develop tools that assist in sifting through all the data to identify information amidst the noise. The two main steps in determining the functional sites in proteins are aligning a large set of homologous sequences and analyzing this large file to identify highly conserved residues. Although a number of tools exist for generating high quality alignments rapidly there are much fewer tools available for rapidly identifying conserved cores within that multiple sequence alignment. PAL, is a Perl script that rapidly identifies conserved residues present in a large alignment file. The strengths of PAL are: speed, flexibility and ease of use.