A novel series of compositionally biased substitution matrices for comparing Plasmodium proteins

Background: The most common substitution matrices currently used (BLOSUM and PAM) are based on protein sequences with average amino acid distributions, thus they do not represent a fully accurate substitution model for proteins characterized by a biased amino acid composition. This problem has been addressed recently by adjusting existing matrices, however, to date, no empirical approach has been taken to build matrices which offer a substitution model for comparing proteins sharing an amino acid compositional bias. Here, we present a novel procedure to construct series of symmetrical substitution matrices to align proteins from similarly biased Plasmodium proteomes. Results: We generated substitution matrices by selecting from the BLOCKS database those multiple alignments with a compositional bias similar to that of P. falciparum and P. yoelii proteins. A novel 'fuzzy' clustering method was adopted to group sequences within these alignments, showing that this method retains...

• Type: Journal
• Year: 2008
• Where: BMCBI
• Authors: Kevin Brick, Elisabetta Pizzi
• Keywords: Amino Acid, BMCBI 2008, Proteins, Substitution Matrices