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

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An Entity of Type : http://linked.opendata.cz/ontology/domain/vavai/Vysledek, within Data Space : linked.opendata.cz associated with source document(s)

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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. The experimental results have shown that a straigh 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. The experimental results have shown that a straigh (en) Indexový přístup k podobnostnímu vyhledávání v proteinových a nukleotidových databázích (cs)
Title	Index-based approach to similarity search in protein and nucleotide databases Indexový přístup k podobnostnímu vyhledávání v proteinových a nukleotidových databázích (cs) 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 Indexový přístup k podobnostnímu vyhledávání v proteinových a nukleotidových databázích (cs) Index-based approach to similarity search in protein and nucleotide databases (en)
skos:notation	RIV/00216208:11320/07:00005162!RIV08-MSM-11320___
http://linked.open.../vavai/riv/strany	67;80
http://linked.open...avai/riv/aktivita	P Z
http://linked.open...avai/riv/aktivity	P(GP201/05/P036), Z(MSM0021620838)
http://linked.open...iv/cisloPeriodika	Neuveden
http://linked.open...vai/riv/dodaniDat	2008
http://linked.open...aciTvurceVysledku	Skopal, Tomáš Hoksza, David
http://linked.open.../riv/druhVysledku	J - Článek v odborném periodiku
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	425967
http://linked.open...ai/riv/idVysledku	RIV/00216208:11320/07:00005162
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...odStatuVydavatele	GB - Spojené království Velké Británie a Severního Irska
http://linked.open...ontrolniKodProRIV	[FA90C13E1BC3]
http://linked.open...i/riv/nazevZdroje	CEUR Workshop Proceedings
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...v/svazekPeriodika	235
http://linked.open...iv/tvurceVysledku	Skopal, Tomáš Hoksza, David
http://linked.open...n/vavai/riv/zamer	Moderní metody, struktury a systémy informatiky
issn	1613-0073
number of pages	14 (xsd:int)
http://localhost/t...ganizacniJednotka	11320

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