PROTOGENE: turning amino acid alignments into bona fide CDS nucleotide alignments.
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ABSTRACT:
SUBMITTER: Moretti S
PROVIDER: S-EPMC1538918 | biostudies-literature | 2006 Jul
REPOSITORIES: biostudies-literature
Publications
PROTOGENE: turning amino acid alignments into bona fide CDS nucleotide alignments.
Moretti Sébastien S Reinier Frédéric F Poirot Olivier O Armougom Fabrice F Audic Stéphane S Keduas Vladimir V Notredame Cédric C
Nucleic acids research 20060701 Web Server issue
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 ...[more]
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