Design, construction and use of the FISH server
2007 (English)In: Applied parallel computing: state of the art in scientific computing, Springer Link , 2007, 647-657 p.Chapter in book (Other academic)
At the core of the FISH (Family Identification with Structure anchored Hidden Markov models, saHMMs) server lies the midnight ASTRAL set. It is a collection of protein domains with low mutual sequence identity within homologous families, according to the structural classification of proteins, SCOP. Here, we evaluate two algorithms for creating the midnight ASTRAL set. The algorithm that limits the number of structural comparisons is about an order of magnitude faster than the all-against-all algorithm. We therefore choose the faster algorithm, although it produces slightly fewer domains in the set. We use the midnight ASTRAL set to construct the structure-anchored Hidden Markov Model data base, saHMM-db, where each saHMM represents one family. Sequence searches using saHMMs provide information about protein function, domain organization, the probable 2D and 3D structure, and can lead to the discovery of homologous domains in remotely related sequences.
Place, publisher, year, edition, pages
Springer Link , 2007. 647-657 p.
, Lecture Notes in Computer Science, ISSN 0302-9743 (Print) 1611-3349 (Online) ; Volume 4699/2010
Bioinformatik, structure-anchored Hidden Markov Model, saHMM, protein structure alignment, protein structure superimposition, remote homologue, FISH-server, protein annotation
Computer Science Bioinformatics and Systems Biology
IdentifiersURN: urn:nbn:se:umu:diva-3126DOI: 10.1007/978-3-540-75755-9_78ISBN: 978-3-540-75754-2OAI: oai:DiVA.org:umu-3126DiVA: diva2:141603
Jeanette Hargbo.2008-04-292008-04-292010-05-10Bibliographically approved