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Design, constructio...
Design, construction and use of the FISH server
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- Tångrot, Jeanette (författare)
- Umeå universitet,Institutionen för datavetenskap,Umeå centrum för molekylär patogenes (UCMP) (Medicinska fakulteten)
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- Wang, Lixiao (författare)
- Umeå universitet,Umeå centrum för molekylär patogenes (UCMP) (Medicinska fakulteten)
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- Kågström, Bo (författare)
- Umeå universitet,Institutionen för datavetenskap,Högpresterande beräkningscentrum norr (HPC2N)
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- Sauer, Uwe H. (författare)
- Umeå universitet,Umeå centrum för molekylär patogenes (UCMP)
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(creator_code:org_t)
- Berlin, Heidelberg : Springer Link, 2007
- 2007
- Engelska.
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Ingår i: Applied parallel computing. - Berlin, Heidelberg : Springer Link. - 9783540757542 ; , s. 647-657
- Relaterad länk:
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https://urn.kb.se/re...
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https://doi.org/10.1...
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Abstract
Ämnesord
Stäng
- 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.
Ämnesord
- NATURVETENSKAP -- Data- och informationsvetenskap -- Datavetenskap (hsv//swe)
- NATURAL SCIENCES -- Computer and Information Sciences -- Computer Sciences (hsv//eng)
- NATURVETENSKAP -- Biologi -- Bioinformatik och systembiologi (hsv//swe)
- NATURAL SCIENCES -- Biological Sciences -- Bioinformatics and Systems Biology (hsv//eng)
Nyckelord
- Bioinformatik
- structure-anchored Hidden Markov Model
- saHMM
- protein structure alignment
- protein structure superimposition
- remote homologue
- FISH-server
- protein annotation
- Computer science
- Datavetenskap
- Bioinformatics
- Bioinformatik
Publikations- och innehållstyp
- vet (ämneskategori)
- kap (ämneskategori)
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