The SYSTERS protein sequence cluster set

Krause A, Stoye J, Vingron M (2000)
Nucleic Acids Research 28(1): 270-272.

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The SYSTERS (short for SYSTEmatic Re-Searching) protein sequence cluster set consists of the classification of all sequences from SWISS-PROT and PIR into disjoint protein family clusters and hierarchically into superfamily and subfamily clusters. The cluster set can be searched with a sequence using the SSMAL search tool or a traditional database search tool like BLAST or FASTA. Additionally a multiple alignment is generated for each cluster and annotated with domain information from the Pfam database of protein domain families. A taxonomic overview of the organisms covered by a cluster is given based on the NCBI taxonomy. The cluster set is available for querying and browsing at http://www.dkfz-heidelberg.de/tbi/services/cluster/systersform
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Krause A, Stoye J, Vingron M. The SYSTERS protein sequence cluster set. Nucleic Acids Research. 2000;28(1):270-272.
Krause, A., Stoye, J., & Vingron, M. (2000). The SYSTERS protein sequence cluster set. Nucleic Acids Research, 28(1), 270-272.
Krause, A., Stoye, J., and Vingron, M. (2000). The SYSTERS protein sequence cluster set. Nucleic Acids Research 28, 270-272.
Krause, A., Stoye, J., & Vingron, M., 2000. The SYSTERS protein sequence cluster set. Nucleic Acids Research, 28(1), p 270-272.
A. Krause, J. Stoye, and M. Vingron, “The SYSTERS protein sequence cluster set”, Nucleic Acids Research, vol. 28, 2000, pp. 270-272.
Krause, A., Stoye, J., Vingron, M.: The SYSTERS protein sequence cluster set. Nucleic Acids Research. 28, 270-272 (2000).
Krause, Antje, Stoye, Jens, and Vingron, Martin. “The SYSTERS protein sequence cluster set”. Nucleic Acids Research 28.1 (2000): 270-272.
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PMID: 25313296
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PMID: 21844638
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PMID: 17217502
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PMID: 16805103
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PMID: 16524831
Sequence-related human proteins cluster by degree of evolutionary conservation.
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PMID: 15600657
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PMID: 11806833

24 References

Data provided by Europe PubMed Central.

Basic local alignment search tool.
Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ., J. Mol. Biol. 215(3), 1990
PMID: 2231712
Gapped BLAST and PSI-BLAST: a new generation of protein database search programs.
Altschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ., Nucleic Acids Res. 25(17), 1997
PMID: 9254694
Improved tools for biological sequence comparison.
Pearson WR, Lipman DJ., Proc. Natl. Acad. Sci. U.S.A. 85(8), 1988
PMID: 3162770
A set-theoretic approach to database searching and clustering.
Krause A, Vingron M., Bioinformatics 14(5), 1998
PMID: 9682056
WWW access to the SYSTERS protein sequence cluster set.
Krause A, Nicodeme P, Bornberg-Bauer E, Rehmsmeier M, Vingron M., Bioinformatics 15(3), 1999
PMID: 10222416

AUTHOR UNKNOWN, 0
Local alignment statistics.
Altschul SF, Gish W., Meth. Enzymol. 266(), 1996
PMID: 8743700

AUTHOR UNKNOWN, 0

AUTHOR UNKNOWN, 0

AUTHOR UNKNOWN, 0

AUTHOR UNKNOWN, 0
The SWISS-PROT protein sequence data bank and its supplement TrEMBL in 1999.
Bairoch A, Apweiler R., Nucleic Acids Res. 27(1), 1999
PMID: 9847139
The PIR-International Protein Sequence Database.
Barker WC, Garavelli JS, McGarvey PB, Marzec CR, Orcutt BC, Srinivasarao GY, Yeh LS, Ledley RS, Mewes HW, Pfeiffer F, Tsugita A, Wu C., Nucleic Acids Res. 27(1), 1999
PMID: 9847137
The Protein Data Bank: a computer-based archival file for macromolecular structures.
Bernstein FC, Koetzle TF, Williams GJ, Meyer EF Jr, Brice MD, Rodgers JR, Kennard O, Shimanouchi T, Tasumi M., J. Mol. Biol. 112(3), 1977
PMID: 875032
The ENZYME data bank in 1999.
Bairoch A., Nucleic Acids Res. 27(1), 1999
PMID: 9847212
The PROSITE database, its status in 1999.
Hofmann K, Bucher P, Falquet L, Bairoch A., Nucleic Acids Res. 27(1), 1999
PMID: 9847184
The EMBL Nucleotide Sequence Database.
Stoesser G, Tuli MA, Lopez R, Sterk P., Nucleic Acids Res. 27(1), 1999
PMID: 9847133
SSMAL: similarity searching with alignment graphs.
Nicodeme P., Bioinformatics 14(6), 1998
PMID: 9694989
Pfam 3.1: 1313 multiple alignments and profile HMMs match the majority of proteins.
Bateman A, Birney E, Durbin R, Eddy SR, Finn RD, Sonnhammer EL., Nucleic Acids Res. 27(1), 1999
PMID: 9847196
GenBank.
Benson DA, Boguski MS, Lipman DJ, Ostell J, Ouellette BF, Rapp BA, Wheeler DL., Nucleic Acids Res. 27(1), 1999
PMID: 9847132
EUCLID: automatic classification of proteins in functional classes by their database annotations.
Tamames J, Ouzounis C, Casari G, Sander C, Valencia A., Bioinformatics 14(6), 1998
PMID: 9694995
MView: a web-compatible database search or multiple alignment viewer.
Brown NP, Leroy C, Sander C., Bioinformatics 14(4), 1998
PMID: 9632837

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