Bioinformatický seminár

Tue 3 Mar. 2009, 17:20

Title: Elemento et al (2007) A universal framework for regulatory element discovery across all genomes and data types
Speaker: Peter Civáň

Budeme diskutovať o článku

Olivier Elemento, Noam Slonim, Saeed Tavazoie. A universal framework for 
regulatory element discovery across all genomes and data types. Molecular
 Cell, 2007

The genomic era has seen a remarkable increase in the number of genomes
being sequenced and annotated. Nonetheless, annotation remains a serious
challenge for compositionally biased genomes. For the preliminary
annotation, popular nucleotide and protein comparison methods such as
BLAST are widely employed. These methods make use of matrices to score
alignments such as the amino acid substitution matrices. Since a
nucleotide bias leads to an overall bias in the amino acid composition of
proteins, it is possible that a genome with nucleotide bias may have
introduced atypical amino acid substitutions in its proteome.
Consequently, standard matrices fail to perform well in sequence analysis
of these genomes. To address this issue, we examined the amino acid
substitution in the AT-rich genome of Plasmodium falciparum, chosen as a
reference and reconstituted a substitution matrix in the genome's context.
The matrix was used to generate protein sequence alignments for the
parasite proteins that improved across the functional regions. We
attribute this to the consistency that may have been achieved amid the
target and background frequencies calculated exclusively in our study.
This study has important implications on annotation of proteins that are
of experimental interest but give poor sequence alignments with standard
conventional matrices.