UniqueProt: creating representative protein sequence sets

UniqueProt is a practical and easy to use web service designed to create representative, unbiased data sets of protein sequences. The largest possible representative sets are found through a simple greedy algorithm using the HSSP-value to establish sequence similarity. UniqueProt is not a real clustering program in the sense that the 'representatives' are not at the centres of well-defined clusters since the definition of such clusters is problem-specific. Overall, UniqueProt is a reasonable fast solution for bias in data sets. The service is accessible at http://cubic.bioc.columbia.edu/services/uniqueprot; a command-line version for Linux is downloadable from this web site.

[1]  C. Chothia,et al.  Assessing sequence comparison methods with reliable structurally identified distant evolutionary relationships. , 1998, Proceedings of the National Academy of Sciences of the United States of America.

[2]  Rolf Apweiler,et al.  The SWISS-PROT protein sequence database and its supplement TrEMBL in 2000 , 2000, Nucleic Acids Res..

[3]  B. Rost.  Twilight zone of protein sequence alignments. , 1999, Protein engineering.

[4]  Annabel E. Todd,et al.  Evolution of function in protein superfamilies, from a structural perspective. , 2001, Journal of molecular biology.

[5]  B Honig,et al.  An integrated approach to the analysis and modeling of protein sequences and structures. II. On the relationship between sequence and structural similarity for proteins that are not obviously related in sequence. , 2000, Journal of molecular biology.

[6]  Adam Godzik,et al.  Clustering of highly homologous sequences to reduce the size of large protein databases , 2001, Bioinform..

[7]  N N Alexandrov,et al.  Statistical significance of ungapped sequence alignments. , 1998, Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing.

[8]  A. Valencia,et al.  Practical limits of function prediction , 2000, Proteins.

[9]  M. Ashburner,et al.  Gene Ontology: tool for the unification of biology , 2000, Nature Genetics.

[10]  M. Gerstein,et al.  Assessing annotation transfer for genomics: quantifying the relations between protein sequence, structure and function through traditional and probabilistic scores. , 2000, Journal of molecular biology.

[11]  Rolf Apweiler,et al.  The SWISS-PROT protein sequence data bank and its supplement TrEMBL , 1997, Nucleic Acids Res..

[12]  B. Rost.  Enzyme function less conserved than anticipated. , 2002, Journal of molecular biology.

[13]  Burkhard Rost,et al.  Sequence conserved for subcellular localization , 2002, Protein science : a publication of the Protein Society.

[14]  Chris Sander,et al.  EUCLID: automatic classification of proteins in functional classes by their database annotations , 1998, Bioinform..

[15]  U. Hobohm,et al.  Enlarged representative set of protein structures , 1994, Protein science : a publication of the Protein Society.

[16]  T. N. Bhat,et al.  The Protein Data Bank , 2000, Nucleic Acids Res..

[17]  C. Sander,et al.  Database of homology‐derived protein structures and the structural meaning of sequence alignment , 1991, Proteins.

[18]  S F Altschul,et al.  Local alignment statistics. , 1996, Methods in enzymology.

[19]  C. Chothia,et al.  Intermediate sequences increase the detection of homology between sequences. , 1997, Journal of molecular biology.

[20]  Anton J. Enright,et al.  GeneRAGE: a robust algorithm for sequence clustering and domain detection , 2000, Bioinform..