PEDANT covers all complete RefSeq genomes

Mathias C Walter; Thomas Rattei; Roland Arnold; Ulrich Güldener; Martin Münsterkötter; Karamfilka Nenova; Gabi Kastenmüller; Patrick Tischler; Andreas Wölling; Andreas Volz; Norbert Pongratz; Ralf Jost; Hans-Werner Mewes; Dmitrij Frishman

doi:10.1093/nar/gkn749

PEDANT covers all complete RefSeq genomes

Mathias C Walter, Thomas Rattei, Roland Arnold, Ulrich Güldener, Martin Münsterkötter, Karamfilka Nenova, Gabi Kastenmüller, Patrick Tischler, Andreas Wölling, Andreas Volz, Norbert Pongratz, Ralf Jost, Hans-Werner Mewes, Dmitrij Frishman

Cancer and Genomic Sciences

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

80 Citations (Scopus)

Abstract

The PEDANT genome database provides exhaustive annotation of nearly 3000 publicly available eukaryotic, eubacterial, archaeal and viral genomes with more than 4.5 million proteins by a broad set of bioinformatics algorithms. In particular, all completely sequenced genomes from the NCBI's Reference Sequence collection (RefSeq) are covered. The PEDANT processing pipeline has been sped up by an order of magnitude through the utilization of precalculated similarity information stored in the similarity matrix of proteins (SIMAP) database, making it possible to process newly sequenced genomes immediately as they become available. PEDANT is freely accessible to academic users at http://pedant.gsf.de. For programmatic access Web Services are available at http://pedant.gsf.de/webservices.jsp.

Original language	English
Pages (from-to)	D408-11
Journal	Nucleic Acids Research
Volume	37
Issue number	Database issue
DOIs	https://doi.org/10.1093/nar/gkn749
Publication status	Published - Jan 2009

Keywords

Databases, Genetic
Genome
Genomics
Internet
Proteins
Journal Article

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10.1093/nar/gkn749

Cite this

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abstract = "The PEDANT genome database provides exhaustive annotation of nearly 3000 publicly available eukaryotic, eubacterial, archaeal and viral genomes with more than 4.5 million proteins by a broad set of bioinformatics algorithms. In particular, all completely sequenced genomes from the NCBI's Reference Sequence collection (RefSeq) are covered. The PEDANT processing pipeline has been sped up by an order of magnitude through the utilization of precalculated similarity information stored in the similarity matrix of proteins (SIMAP) database, making it possible to process newly sequenced genomes immediately as they become available. PEDANT is freely accessible to academic users at http://pedant.gsf.de. For programmatic access Web Services are available at http://pedant.gsf.de/webservices.jsp.",

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AU - Walter, Mathias C

AU - Rattei, Thomas

AU - Arnold, Roland

AU - Güldener, Ulrich

AU - Münsterkötter, Martin

AU - Nenova, Karamfilka

AU - Kastenmüller, Gabi

AU - Tischler, Patrick

AU - Wölling, Andreas

AU - Volz, Andreas

AU - Pongratz, Norbert

AU - Jost, Ralf

AU - Mewes, Hans-Werner

AU - Frishman, Dmitrij

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N2 - The PEDANT genome database provides exhaustive annotation of nearly 3000 publicly available eukaryotic, eubacterial, archaeal and viral genomes with more than 4.5 million proteins by a broad set of bioinformatics algorithms. In particular, all completely sequenced genomes from the NCBI's Reference Sequence collection (RefSeq) are covered. The PEDANT processing pipeline has been sped up by an order of magnitude through the utilization of precalculated similarity information stored in the similarity matrix of proteins (SIMAP) database, making it possible to process newly sequenced genomes immediately as they become available. PEDANT is freely accessible to academic users at http://pedant.gsf.de. For programmatic access Web Services are available at http://pedant.gsf.de/webservices.jsp.

AB - The PEDANT genome database provides exhaustive annotation of nearly 3000 publicly available eukaryotic, eubacterial, archaeal and viral genomes with more than 4.5 million proteins by a broad set of bioinformatics algorithms. In particular, all completely sequenced genomes from the NCBI's Reference Sequence collection (RefSeq) are covered. The PEDANT processing pipeline has been sped up by an order of magnitude through the utilization of precalculated similarity information stored in the similarity matrix of proteins (SIMAP) database, making it possible to process newly sequenced genomes immediately as they become available. PEDANT is freely accessible to academic users at http://pedant.gsf.de. For programmatic access Web Services are available at http://pedant.gsf.de/webservices.jsp.

KW - Databases, Genetic

KW - Genome

KW - Genomics

KW - Internet

KW - Proteins

KW - Journal Article

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DO - 10.1093/nar/gkn749

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SP - D408-11

JO - Nucleic Acids Research

JF - Nucleic Acids Research

IS - Database issue

ER -

PEDANT covers all complete RefSeq genomes

Abstract

Keywords

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