Bioinformatics Vol. 19 no. 12 2003
Pages 1589-1591
© 2003 Oxford University Press
Applications Note |
PISCES: a protein sequence culling server
Institute for Cancer Research, Fox Chase Cancer Center, 7701 Burholme Avenue, Philadelphia, PA 19111, USA
Received on October 4, 2002
; revised on January 30, 2003
; accepted on March 18, 2003
Summary: PISCES is a public server for culling sets of protein sequences from the Protein Data Bank (PDB) by sequence identity and structural quality criteria. PISCES can provide lists culled from the entire PDB or from lists of PDB entries or chains provided by the user. The sequence identities are obtained from PSI-BLAST alignments with position-specific substitution matrices derived from the non-redundant protein sequence database. PISCES therefore provides better lists than servers that use BLAST, which is unable to identify many relationships below 40% sequence identity and often overestimates sequence identity by aligning only well-conserved fragments. PDB sequences are updated weekly. PISCES can also cull non-PDB sequences provided by the user as a list of GenBank identifiers, a FASTA format file, or BLAST/PSI-BLAST output.
Availability: The server is located at http://www.fccc.edu/research/labs/dunbrack/pisces
Contact: rl_dunbrack{at}fccc.edu
* To whom correspondence should be addressed.
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