TreeDet: a web server to explore sequence space | Zendy

A. Carro | Zendy; Michael L. Tress | Zendy; David Juan | Zendy; Florencio Pazos | Zendy; Pedro LópezRomero | Zendy; Antonio del Sol | Zendy; Alfonso Valencia | Zendy; Ana M. Rojas | Zendy

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TreeDet: a web server to explore sequence space

Author(s) -

A. Carro,

Michael L. Tress,

David Juan,

Florencio Pazos,

Pedro LópezRomero,

Antonio del Sol,

Alfonso Valencia,

Ana M. Rojas

Publication year - 2006

Publication title -

nucleic acids research

Language(s) - English

Resource type - Journals

SCImago Journal Rank - 9.008

H-Index - 537

eISSN - 1362-4954

pISSN - 0305-1048

DOI - 10.1093/nar/gkl203

Subject(s) - web server , biology , upload , sequence (biology) , server , tree (set theory) , relation (database) , conserved sequence , computational biology , computer science , data mining , base sequence , genetics , the internet , operating system , mathematics , combinatorics , dna

The TreeDet (Tree Determinant) Server is the first release of a system designed to integrate results from methods that predict functional sites in protein families. These methods take into account the relation between sequence conservation and evolutionary importance. TreeDet fully analyses the space of protein sequences in either user-uploaded or automatically generated multiple sequence alignments. The methods implemented in the server represent three main classes of methods for the detection of family-dependent conserved positions, a tree-based method, a correlation based method and a method that employs a principal component analyses coupled to a cluster algorithm. An additional method is provided to highlight the reliability of the position in the alignments. The server is available at http://www.pdg.cnb.uam.es/servers/treedet.

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