SYSTERS, GeneNest, SpliceNest: exploring sequence space from genome to protein - PubMed (original) (raw)

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

Antje Krause et al. Nucleic Acids Res. 2002.

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.

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Figures

Figure 1

The integration of SYSTERS, GeneNest and SpliceNest into one framework. Possible queries to the databases are given on the left (blue), followed by the underlying query tools BLAST and SSMAL (green). The features and interactions of the SYSTERS, GeneNest and SpliceNest databases are shown in the middle (yellow) and links to external resources on the right (red).

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References

1. 1. Krause A. and Vingron,M. (1998) A set-theoretic approach to database searching and clustering. Bioinformatics, 14, 430–438. - PubMed
2. 1. Bairoch A. and Apweiler,R. (2000) The SWISS-PROT protein sequence database and its supplement TrEMBL in 2000. Nucleic Acids Res., 28, 45–48. - PMC - PubMed
3. 1. Barker W.C., Garavelli,J.S., Hou,Z., Huang,H., Ledley,R.S., McGarvey,P.B., Mewes,H.W., Orcutt,B.C., Pfeiffer,F., Tsugita,A. et al. (2001) Protein Information Resource: a community resource for expert annotation of protein data. Nucleic Acids Res., 29, 29–32. Updated article in this issue: Nucleic Acids Res. (2002), 30, 35–37. - PMC - PubMed
4. 1. Altschul S.F., Madden,T.L., Schäffer,A.A., Zhang,J., Zhang,Z., Miller,W. and Lipman,D.J. (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res., 25, 3389–3402. - PMC - PubMed
5. 1. Thompson J.D., Higgins,D.G. and Gibson,T.J. (1994) CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position specific gap penalties and weight matrix choice. Nucleic Acids Res., 22, 4673–4680. - PMC - PubMed

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