Blast sampling for structural and functional analyses

Background: The post-genomic era is characterised by a torrent of biological information flooding the public databases. As a direct consequence, similarity searches starting with a single query sequence frequently lead to the identification of hundreds, or even thousands of potential homologues. The huge volume of data renders the subsequent structural, functional and evolutionary analyses very difficult. It is therefore essential to develop new strategies for efficient sampling of this large sequence space, in order to reduce the number of sequences to be processed. At the same time, it is important to retain the most pertinent sequences for structural and functional studies. Results: An exhaustive analysis on a large scale test set (284 protein families) was performed to compare the efficiency of four different sampling methods aimed at selecting the most pertinent sequences. These four methods sample the proteins detected by BlastP searches and can be divided into two categories: t...

• Type: Journal
• Year: 2007
• Where: BMCBI
• Authors: Anne Friedrich, Raymond Ripp, Nicolas Garnier, Emmanuel Bettler, Gilbert Deléage, Olivier Poch, Luc Moulinier
• Keywords: BMCBI 2007, Pertinent Sequences, Sampling Methods, Sequences