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

ABSTRACT:

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 wit

SUBMITTER: Brick K 

PROVIDER: S-EPMC2408606 | biostudies-literature | 2008 May

REPOSITORIES: biostudies-literature