AUGUSTUS: a web server for gene prediction in eukaryotes that allows user-defined constraints.
Nucleic Acids Res
; 33(Web Server issue): W465-7, 2005 Jul 01.
Article
em En
| MEDLINE
| ID: mdl-15980513
ABSTRACT
We present a WWW server for AUGUSTUS, a software for gene prediction in eukaryotic genomic sequences that is based on a generalized hidden Markov model, a probabilistic model of a sequence and its gene structure. The web server allows the user to impose constraints on the predicted gene structure. A constraint can specify the position of a splice site, a translation initiation site or a stop codon. Furthermore, it is possible to specify the position of known exons and intervals that are known to be exonic or intronic sequence. The number of constraints is arbitrary and constraints can be combined in order to pin down larger parts of the predicted gene structure. The result then is the most likely gene structure that complies with all given user constraints, if such a gene structure exists. The specification of constraints is useful when part of the gene structure is known, e.g. by expressed sequence tag or protein sequence alignments, or if the user wants to change the default prediction. The web interface and the downloadable stand-alone program are available free of charge at http//augustus.gobics.de/submission.
Texto completo:
1
Temas:
ECOS
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Financiamentos_gastos
Bases de dados:
MEDLINE
Assunto principal:
Software
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Genômica
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Genes
Tipo de estudo:
Health_economic_evaluation
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Prognostic_studies
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Risk_factors_studies
Limite:
Animals
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Humans
Idioma:
En
Revista:
Nucleic Acids Res
Ano de publicação:
2005
Tipo de documento:
Article
País de afiliação:
Alemanha