PC/GENE: Sequence Comparisons and Homologies

Generally, the purpose of aligning sequences is to determine the phylogenetic relationship between the sequences and/or to identify conserved regions that may represent biologically functional domains. The PC/GENE package contains three programs that help to determine the optimal alignment of nucleic acid and protein sequences. NALIGN will align two nucleic acid sequences, and PALIGN will align two protein sequences. Both programs will impose gaps, within user-defined constraints, to optimize the alignments. In addition, PALIGN will allow partial weight for similar amino acids. The third program, CLUSTAL, will align both nucleic acid and protein sequences. CLUSTAL can align up to 25 sequences, and in addition to showing the sequence alignments, CLUSTAL will draw a dendrogram to illustrate the phylogenetic relationship between the aligned sequences.