EVEREST: automatic identification and classification of protein domains in all protein sequences
نویسندگان
چکیده
منابع مشابه
Automatic Identification and Classification of Protein Domains
Motivation: Proteins are comprised of one or several domains. Such domains can be classified into families according to their biological function. Whereas sequencing technologies have advanced immensely in recent years, there are no matching computational tools for large-scale determination of protein domains and their boundaries. The present paper addresses the challenge of developing computat...
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We investigate the space of all protein sequences. We combine the standard measures of similarity (SW, FASTA, BLAST), to associate with each sequence an exhaustive list of neighboring sequences. These lists induce a (weighted directed) graph whose vertices are the sequences. The weight of an edge connecting two sequences represents their degree of similarity. This graph encodes much of the fund...
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Discovering Domains Mediating Protein Interactions
Background: Protein-protein interactions do not provide any direct information regarding the domains within the proteins that mediate the interactions. The majority of proteins are multi domain proteins and the interaction between them is often defined by the pairs of their domains. Most of the former studies focus only on interacting domain pairs. However they do not consider the in...
متن کاملEVEREST: a collection of evolutionary conserved protein domains
Protein domains are subunits of proteins that recur throughout the protein world. There are many definitions attempting to capture the essence of a protein domain, and several systems that identify protein domains and classify them into families. EVEREST, recently described in Portugaly et al. (2006) BMC Bioinformatics, 7, 277, is one such system that performs the task automatically, using prot...
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ژورنال
عنوان ژورنال: BMC Bioinformatics
سال: 2006
ISSN: 1471-2105
DOI: 10.1186/1471-2105-7-277