Scoring Amino Acid Substitutions In Φhage Genomes
نویسنده
چکیده
Substitution matrices are among the most widely used scoring techniques : BLAST, Muscle and other alignment packages, all use them. However these matrices are general; they ignore organism specific properties and do not provide customized scoring schemes. We present a Φhage-specific scoring matrix based on the abundances of aligned substitutions. These matrices use information from approximately five and a half million similar protein alignments from over five hundred Φhage genomes. Our scoring matrix is different from the existing PAM and BLOSUM matrices. This indicates the need for similar treatments for other groups of organisms.
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