title: PROTOGENE: turning amino acid alignments into bona fide CDS nucleotide alignments.
abstract: We describe Protogene, a server that can turn a protein multiple sequence alignment into the equivalent alignment of the original gene coding DNA. Protogene relies on a pipeline where every initial protein sequence is BLASTed against RefSeq or NR. The annotation associated with potential matches is used to identify the gene sequence. This gene sequence is then aligned with the query protein using Exonerate in order to extract a coding nucleotide sequence matching the original protein. Protogene can handle protein fragments and will return every CDS coding for a given protein, even if they occur in different genomes. Protogene is available from http://www.tcoffee.org/.
authors.affiliation: Information Génomique et Structurale, CNRS UPR2589, Institute for Structural Biology and Microbiology (IBSM), Parc Scientifique de Luminy, 163 Avenue de Luminy, FR 13288, Marseille cedex 09, France.
authors.forename: Sébastien
authors.initials: S
authors.lastname: Moretti
authors.forename: Frédéric
authors.initials: F
authors.lastname: Reinier
authors.forename: Olivier
authors.initials: O
authors.lastname: Poirot
authors.forename: Fabrice
authors.initials: F
authors.lastname: Armougom
authors.forename: Stéphane
authors.initials: S
authors.lastname: Audic
authors.forename: Vladimir
authors.initials: V
authors.lastname: Keduas
authors.forename: Cédric
authors.initials: C
authors.lastname: Notredame
mesh_terms: D001483:Base Sequence; D004247:DNA / Q000737:chemistry; D005796:Genes; D020407:Internet; D012333:RNA, Messenger / Q000737:chemistry; D016415:Sequence Alignment / Q000379:methods*; D020539:Sequence Analysis, Protein; D012984:Software; D014584:User-Computer Interface
chemical_list: D012333:RNA, Messenger; D004247:DNA