About: Index-based approach to similarity search in protein and nucleotide databases

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rdf:type	skos:Concept http://linked.opendata.cz/ontology/domain/vavai/Vysledek
Description	When searching databases of nucleotide or protein sequences, finding a local alignment of two sequences is one of the main tasks. Since the sizes of available databases grow constantly, the efficiency of retrieval methods becomes the critical issue. The sequence retrieval relies on finding sequences in the database which align best with the query sequence. However, an optimal alignment can be found in quadratic time (by use of dynamic programming) while this is infeasible when dealing with large databases. The existing solutions use fast heuristic methods (like BLAST, FASTA) which produce only an uncontrolled approximation of the best alignment and even do not provide any information about the alignment approximation error. In this paper we propose an approach of exact and approximate indexing using several metric access methods (MAMs) in combination with the TriGen algorithm, in order to reduce the number of alignments (distance computations) needed. When searching databases of nucleotide or protein sequences, finding a local alignment of two sequences is one of the main tasks. Since the sizes of available databases grow constantly, the efficiency of retrieval methods becomes the critical issue. The sequence retrieval relies on finding sequences in the database which align best with the query sequence. However, an optimal alignment can be found in quadratic time (by use of dynamic programming) while this is infeasible when dealing with large databases. The existing solutions use fast heuristic methods (like BLAST, FASTA) which produce only an uncontrolled approximation of the best alignment and even do not provide any information about the alignment approximation error. In this paper we propose an approach of exact and approximate indexing using several metric access methods (MAMs) in combination with the TriGen algorithm, in order to reduce the number of alignments (distance computations) needed. (en)
Title	Index-based approach to similarity search in protein and nucleotide databases Index-based approach to similarity search in protein and nucleotide databases (en)
skos:prefLabel	Index-based approach to similarity search in protein and nucleotide databases Index-based approach to similarity search in protein and nucleotide databases (en)
skos:notation	RIV/00216208:11320/07:00206200!RIV10-GA0-11320___
http://linked.open...avai/riv/aktivita	P Z
http://linked.open...avai/riv/aktivity	P(GP201/05/P036), Z(MSM0021620838)
http://linked.open...vai/riv/dodaniDat	2010
http://linked.open...aciTvurceVysledku	Skopal, Tomáš Hoksza, David
http://linked.open.../riv/druhVysledku	D - Článek ve sborníku
http://linked.open...iv/duvernostUdaju	S - Úplné a pravdivé údaje nepodléhající ochraně podle zvláštních právních předpisů
http://linked.open...titaPredkladatele	Univerzita Karlova v Praze / Matematicko-fyzikální fakulta
http://linked.open...dnocenehoVysledku	425966
http://linked.open...ai/riv/idVysledku	RIV/00216208:11320/07:00206200
http://linked.open...riv/jazykVysledku	eng - angličtina
http://linked.open.../riv/klicovaSlova	Index-based; approach; similarity; search; protein; nucleotide; databases (en)
http://linked.open.../riv/klicoveSlovo	Index-based protein similarity databases search approach nucleotide
http://linked.open...ontrolniKodProRIV	[52B44C12DADA]
http://linked.open...v/mistoKonaniAkce	Neuveden
http://linked.open...i/riv/nazevZdroje	DATESO 2007
http://linked.open...in/vavai/riv/obor	JC
http://linked.open...ichTvurcuVysledku	2 (xsd:int)
http://linked.open...cetTvurcuVysledku	2 (xsd:int)
http://linked.open...vavai/riv/projekt	Efficient metric search in large multimedia databases
http://linked.open...UplatneniVysledku	2007
http://linked.open...iv/tvurceVysledku	Skopal, Tomáš Hoksza, David
http://linked.open...vavai/riv/typAkce	EUR - Evropská
http://linked.open...ain/vavai/riv/wos	000272455400007
http://linked.open.../riv/zahajeniAkce	2007-01-01 (xsd:date)
http://linked.open...n/vavai/riv/zamer	Moderní metody, struktury a systémy informatiky
number of pages	14 (xsd:int)
http://purl.org/ne...btex#hasPublisher	Matfyz Press, Praha
https://schema.org/isbn	978-80-7378-002-9
http://localhost/t...ganizacniJednotka	11320
is http://linked.open...avai/riv/vysledek of	Index-based approach to similarity search in protein and nucleotide databases Index-based approach to similarity search in protein and nucleotide databases Index-based approach to similarity search in protein and nucleotide databases

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