AGenDA: homology-based gene prediction

Leila Taher; Oliver Rinner; Saurabh Garg; Alexander Sczyrba; Michael Brudno; Serafim Batzoglou; Burkhard Morgenstern

doi:10.1093/bioinformatics/btg181

AGenDA: homology-based gene prediction

Leila Taher, Oliver Rinner, Saurabh Garg, Alexander Sczyrba, Michael Brudno, Serafim Batzoglou, Burkhard Morgenstern

Institut für Biomedical Informatics (7200)

Publikation: Beitrag in einer Fachzeitschrift › Artikel › Begutachtung

Abstract

We present a www server for homology-based gene prediction. The user enters a pair of evolutionary related genomic sequences, for example from human and mouse. Our software system uses CHAOS and DIALIGN to calculate an alignment of the input sequences and then searches for conserved splicing signals and start/stop codons around regions of local sequence similarity. This way, candidate exons are identified that are used, in turn, to calculate optimal gene models. The server returns the constructed gene model by email, together with a graphical representation of the underlying genomic alignment.

Originalsprache	englisch
Seiten (von - bis)	1575-7
Seitenumfang	3
Fachzeitschrift	Bioinformatics
Jahrgang	19
Ausgabenummer	12
DOIs	https://doi.org/10.1093/bioinformatics/btg181
Publikationsstatus	Veröffentlicht - 12 Aug. 2003

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10.1093/bioinformatics/btg181

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abstract = "We present a www server for homology-based gene prediction. The user enters a pair of evolutionary related genomic sequences, for example from human and mouse. Our software system uses CHAOS and DIALIGN to calculate an alignment of the input sequences and then searches for conserved splicing signals and start/stop codons around regions of local sequence similarity. This way, candidate exons are identified that are used, in turn, to calculate optimal gene models. The server returns the constructed gene model by email, together with a graphical representation of the underlying genomic alignment.",

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author = "Leila Taher and Oliver Rinner and Saurabh Garg and Alexander Sczyrba and Michael Brudno and Serafim Batzoglou and Burkhard Morgenstern",

year = "2003",

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doi = "10.1093/bioinformatics/btg181",

language = "English",

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T2 - homology-based gene prediction

AU - Taher, Leila

AU - Rinner, Oliver

AU - Garg, Saurabh

AU - Sczyrba, Alexander

AU - Brudno, Michael

AU - Batzoglou, Serafim

AU - Morgenstern, Burkhard

PY - 2003/8/12

Y1 - 2003/8/12

N2 - We present a www server for homology-based gene prediction. The user enters a pair of evolutionary related genomic sequences, for example from human and mouse. Our software system uses CHAOS and DIALIGN to calculate an alignment of the input sequences and then searches for conserved splicing signals and start/stop codons around regions of local sequence similarity. This way, candidate exons are identified that are used, in turn, to calculate optimal gene models. The server returns the constructed gene model by email, together with a graphical representation of the underlying genomic alignment.

AB - We present a www server for homology-based gene prediction. The user enters a pair of evolutionary related genomic sequences, for example from human and mouse. Our software system uses CHAOS and DIALIGN to calculate an alignment of the input sequences and then searches for conserved splicing signals and start/stop codons around regions of local sequence similarity. This way, candidate exons are identified that are used, in turn, to calculate optimal gene models. The server returns the constructed gene model by email, together with a graphical representation of the underlying genomic alignment.

KW - Algorithms

KW - Electronic Mail

KW - Evolution, Molecular

KW - Gene Expression Profiling/methods

KW - Information Storage and Retrieval/methods

KW - Internet

KW - Models, Genetic

KW - Phylogeny

KW - Sequence Alignment/methods

KW - Sequence Analysis, DNA/methods

KW - Sequence Homology, Nucleic Acid

KW - Software

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DO - 10.1093/bioinformatics/btg181

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SN - 1367-4803

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JO - Bioinformatics

JF - Bioinformatics

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ER -

AGenDA: homology-based gene prediction

Abstract

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