PROTOGENE: turning amino acid alignments into bona fide CDS nucleotide alignments

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...

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Bibliographic Details
Published in:Nucleic acids research 2006-07, Vol.34 (suppl-2), p.W600-W603
Main Authors: Moretti, Sébastien, Reinier, Frédéric, Poirot, Olivier, Armougom, Fabrice, Audic, Stéphane, Keduas, Vladimir, Notredame, Cédric
Format: Article
Language:English
Subjects:
Base Sequence
DNA - chemistry
Genes
Internet
RNA, Messenger - chemistry
Sequence Alignment - methods
Sequence Analysis, Protein
Software
User-Computer Interface
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Description
Summary: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/.
ISSN:0305-1048
1362-4962
DOI:10.1093/nar/gkl170