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

Institute of Biomedical Informatics (7200)

Research output: Contribution to journal › Article › peer-review

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.

Original language	English
Pages (from-to)	1575-7
Number of pages	3
Journal	Bioinformatics
Volume	19
Issue number	12
DOIs	https://doi.org/10.1093/bioinformatics/btg181
Publication status	Published - 12 Aug 2003

Keywords

Algorithms
Electronic Mail
Evolution, Molecular
Gene Expression Profiling/methods
Information Storage and Retrieval/methods
Internet
Models, Genetic
Phylogeny
Sequence Alignment/methods
Sequence Analysis, DNA/methods
Sequence Homology, Nucleic Acid
Software

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10.1093/bioinformatics/btg181

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title = "AGenDA: homology-based gene prediction",

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.",

keywords = "Algorithms, Electronic Mail, Evolution, Molecular, Gene Expression Profiling/methods, Information Storage and Retrieval/methods, Internet, Models, Genetic, Phylogeny, Sequence Alignment/methods, Sequence Analysis, DNA/methods, Sequence Homology, Nucleic Acid, Software",

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",

volume = "19",

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journal = "Bioinformatics",

issn = "1367-4803",

publisher = "Oxford University Press",

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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

M3 - Article

C2 - 12912840

SN - 1367-4803

VL - 19

SP - 1575

EP - 1577

JO - Bioinformatics

JF - Bioinformatics

IS - 12

ER -

AGenDA: homology-based gene prediction

Abstract

Keywords

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