leBIBIQBPP: a set of databases and a webtool for automatic phylogenetic analysis of prokaryotic sequences.
BACKGROUND
Estimating the phylogenetic position of bacterial and archaeal organisms by genetic sequence comparisons is considered as the gold-standard in taxonomy. This is also a way to identify the species of origin of the sequence. The quality of the reference database used in such analyses is crucial: the database must reflect the up-to-date bacterial nomenclature and accurately indicate the species of origin of its sequences.


METHODS
leBIBI(QBPP) is a web tool taking as input a series of nucleotide sequences belonging to one of a set of reference markers (e.g., SSU rRNA, rpoB, groEL2) and automatically retrieving closely related sequences, aligning them, and performing phylogenetic reconstruction using an approximate maximum likelihood approach. The system returns a set of quality parameters and, if possible, a suggested taxonomic assigment for the input sequences. The reference databases are extracted from GenBank and present four degrees of stringency, from the "superstringent" degree (one type strain per species) to the loosely parsed degree ("lax" database). A set of one hundred to more than a thousand sequences may be analyzed at a time. The speed of the process has been optimized through careful hardware selection and database design.


CONCLUSIONS
leBIBI(QBPP) is a powerful tool helping biologists to position bacterial or archaeal sequence commonly used markers in a phylogeny. It is a diagnostic tool for clinical, industrial and environmental microbiology laboratory, as well as an exploratory tool for more specialized laboratories. Its main advantages, relatively to comparable systems are: i) the use of a broad set of databases covering diverse markers with various degrees of stringency; ii) the use of an approximate Maximum Likelihood approach for phylogenetic reconstruction; iii) a speed compatible with on-line usage; and iv) providing fully documented results to help the user in decision making.
Laboratoire de Biométrie et Biologie Evolutive, UMR CNRS 5558, Université Claude Bernard - Lyon 1, 43 bd. du 11 Novembre 1918, Villeurbanne, 69622, France. jean-pierre.flandrois@univ-lyon1.fr.
Jean-Pierre
JP
Flandrois
Laboratoire de Biométrie et Biologie Evolutive, UMR CNRS 5558, Université Claude Bernard - Lyon 1, 43 bd. du 11 Novembre 1918, Villeurbanne, 69622, France. guy.perriere@univ-lyon1.fr.
Guy
G
Perrière
Laboratoire de Biométrie et Biologie Evolutive, UMR CNRS 5558, Université Claude Bernard - Lyon 1, 43 bd. du 11 Novembre 1918, Villeurbanne, 69622, France. manolo.gouy@univ-lyon1.fr.
Manolo
M
Gouy
D001105:Archaea / Q000145:classification / Q000235:genetics*; D001419:Bacteria / Q000145:classification / Q000235:genetics*; D019295:Computational Biology; D030561:Databases, Nucleic Acid; D020407:Internet; D016013:Likelihood Functions; D010802:Phylogeny; D019642:RNA, Archaeal / Q000235:genetics; D012329:RNA, Bacterial / Q000235:genetics; D012335:RNA, Ribosomal / Q000235:genetics; D017423:Sequence Analysis, RNA / Q000379:methods*; D012984:Software
D019642:RNA, Archaeal; D012329:RNA, Bacterial; D012335:RNA, Ribosomal