EVEREST - EVolutionary Ensembles of REcurrent SegmenTs
NAR Molecular Biology Database Collection entry number 963
Portugaly E.1Linial N.1 and Linial M.2
1School of Computer Science & Engineering, The Hebrew University of Jerusalem, Israel
2Dept. of Biological Chemistry, Inst. of Life Sciences, The Hebrew University of Jerusalem, Israel
2Dept. of Biological Chemistry, Inst. of Life Sciences, The Hebrew University of Jerusalem, Israel
Contact elonp@cs.huji.ac.il
Database Description
EVEREST is an automatic computational process identifying protein domainsand classifying them into families. The EVEREST database contains 20,029families, each defined by one or more HMMER HMMs. EVEREST has beenthoroughly tested and evaluated, and has been shown to reconstruct 56% ofPfam A families and 63% of SCOP families with high accuracy, and tosuggest many new domain families.
The current release of the EVEREST database was constructed by scanningUniProt release 8.1 and the sequences of all PDB structures with each ofthe EVEREST families.
The EVEREST database of protein domain families can be accessed throughthe EVEREST website. The web-site allows browsing through EVEREST domainfamilies as well as domain families defined by SCOP, CATH and Pfam A. Afamily page in the website provides a graphical representation of allproteins containing a domain of the family, and of all domains, as definedby the above four domain definition systems, on these proteins. Thewebsite also features analysis of relationship between families andsearches for proteins and families on the basis of keywords, familystatistics, family phylogenetic profile and more. Finally, the user mayupload a sequence to be scanned for EVEREST families and stored for futurebrowsing by that user.
The EVEREST database is also available for download in flat file format.
The current release of the EVEREST database was constructed by scanningUniProt release 8.1 and the sequences of all PDB structures with each ofthe EVEREST families.
The EVEREST database of protein domain families can be accessed throughthe EVEREST website. The web-site allows browsing through EVEREST domainfamilies as well as domain families defined by SCOP, CATH and Pfam A. Afamily page in the website provides a graphical representation of allproteins containing a domain of the family, and of all domains, as definedby the above four domain definition systems, on these proteins. Thewebsite also features analysis of relationship between families andsearches for proteins and families on the basis of keywords, familystatistics, family phylogenetic profile and more. Finally, the user mayupload a sequence to be scanned for EVEREST families and stored for futurebrowsing by that user.
The EVEREST database is also available for download in flat file format.
Acknowledgements
While developing EVEREST, E.P. was supported by an Eshkol fellowship from the Israeli Ministry of Science and by the Sudarsky B Center for Computational Biology.
This work is partially funded by NoE (Framework VI) BioSapiens consortium.
This work is partially funded by NoE (Framework VI) BioSapiens consortium.
References
1. Portugaly, E., Linial, N. and Linial, M. (2007) EVEREST: A collection of evolutionary conserved protein domains. Nucleic Acids Res, 35: in press.
2. Portugaly,E., Harel,A., Linial,N. and Linial,M. (2006) EVEREST: automatic identification and classification of protein domains in all protein sequences. BMC Bioinformatics, 7: 277.
2. Portugaly,E., Harel,A., Linial,N. and Linial,M. (2006) EVEREST: automatic identification and classification of protein domains in all protein sequences. BMC Bioinformatics, 7: 277.
Category: Protein sequence databases
Subcategory: Protein domain databases; protein classification
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