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

Details

Serval ID
serval:BIB_F1F82A40F52D
Type
Article: article from journal or magazin.
Collection
Publications
Title
PROTOGENE: turning amino acid alignments into bona fide CDS nucleotide alignments.
Journal
Nucleic Acids Research
Author(s)
Moretti S., Reinier F., Poirot O., Armougom F., Audic S., Keduas V., Notredame C.
ISSN
1362-4962[electronic]
Publication state
Published
Issued date
07/2006
Volume
34
Number
Web Server issue
Pages
W600-W603
Language
english
Notes
Publication types: Journal Article
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/.
Keywords
Base Sequence, DNA/chemistry, Genes, Internet, RNA, Messenger/chemistry, Sequence Alignment/methods, Sequence Analysis, Protein, Software, User-Computer Interface
Pubmed
Open Access
Yes
Create date
19/11/2007 10:53
Last modification date
20/08/2019 16:19
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