Sciweavers

Share
BMCBI
2008

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

8 years 5 months ago
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...
Kevin Brick, Elisabetta Pizzi
Added 08 Dec 2010
Updated 08 Dec 2010
Type Journal
Year 2008
Where BMCBI
Authors Kevin Brick, Elisabetta Pizzi
Comments (0)
books