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Literature DB >> 11752319

SYSTERS, GeneNest, SpliceNest: exploring sequence space from genome to protein.

Antje Krause¹, Stefan A Haas, Eivind Coward, Martin Vingron.

Abstract

We have integrated the protein families from SYSTERS and the expressed sequence tag (EST) clusters from our database GeneNest with SpliceNest, a new database mapping EST contigs into genomic DNA. The SYSTERS protein sequence cluster set provides an automatically generated classification of all sequences of the SWISS-PROT, TrEMBL and PIR databases into disjoint protein family and superfamily clusters. GeneNest is a database and software package for producing and visualizing gene indices from ESTs and mRNAs. Currently, the database comprises gene indices of human, mouse, Arabidopsis thaliana and zebrafish. SpliceNest is a web-based graphical tool to explore gene structure, including alternative splicing, based on a mapping of the EST consensus sequences from GeneNest to the complete human genome. The integration of SYSTERS, GeneNest and SpliceNest into one framework now permits an overall exploration of the whole sequence space covering protein, mRNA and EST sequences, as well as genomic DNA. The databases are available for querying and browsing at http://cmb.molgen.mpg.de.

Entities: Species

Mesh：

Substances：
Proteins
RNA, Messenger

Year: 2002 PMID： 11752319 PMCID： PMC99107 DOI： 10.1093/nar/30.1.299

Source DB: PubMed Journal: Nucleic Acids Res ISSN： 0305-1048 Impact factor: 16.971

13 in total

1. The Pfam protein families database.

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Journal: Nucleic Acids Res Date: 2000-01-01 Impact factor: 16.971

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Journal: Nucleic Acids Res Date: 2001-01-01 Impact factor: 16.971

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Journal: Nucleic Acids Res Date: 2001-01-01 Impact factor: 16.971

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Journal: Nature Date: 2001-02-15 Impact factor: 49.962

5. GeneNest: automated generation and visualization of gene indices.

Authors: S A Haas; T Beissbarth; E Rivals; A Krause; M Vingron
Journal: Trends Genet Date: 2000-11 Impact factor: 11.639

6. The SWISS-PROT protein sequence database and its supplement TrEMBL in 2000.

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Journal: Nucleic Acids Res Date: 2000-01-01 Impact factor: 16.971

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Journal: J Mol Med (Berl) Date: 1997-10 Impact factor: 4.599

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Journal: Nucleic Acids Res Date: 1997-09-01 Impact factor: 16.971

21 in total

1. PHYTOPROT: a database of clusters of plant proteins.

Authors: S Mohseni-Zadeh; A Louis; P Brézellec; J-L Risler
Journal: Nucleic Acids Res Date: 2004-01-01 Impact factor: 16.971

2. Protein families and TRIBES in genome sequence space.

Authors: Anton J Enright; Victor Kunin; Christos A Ouzounis
Journal: Nucleic Acids Res Date: 2003-08-01 Impact factor: 16.971

3. ASmodeler: gene modeling of alternative splicing from genomic alignment of mRNA, EST and protein sequences.

Authors: Namshin Kim; Seokmin Shin; Sanghyuk Lee
Journal: Nucleic Acids Res Date: 2004-07-01 Impact factor: 16.971

4. The Cell Wall Navigator database. A systems-based approach to organism-unrestricted mining of protein families involved in cell wall metabolism.

Authors: Thomas Girke; Josh Lauricha; Hua Tran; Kenneth Keegstra; Natasha Raikhel
Journal: Plant Physiol Date: 2004-10 Impact factor: 8.340