Multi-seed lossless filtration
Identifieur interne : 000666 ( Crin/Checkpoint ); précédent : 000665; suivant : 000667Multi-seed lossless filtration
Auteurs : Gregory Kucherov ; Laurent Noé ; Mikhail RoytbergSource :
English descriptors
- KwdEn :
Abstract
We study a method of seed-based lossless filtration for approximate string matching and related applications. The method is based on a simultaneous use of several spaced seeds rather than a single seed as studied by Burkhardt and Karkkainen. We present algorithms to compute several important parameters of seed families, study their combinatorial properties, and describe several techniques to construct efficient families. We also report a large-scale application of the proposed technique to the problem of oligonucleotide selection for an EST sequence database.
Links toward previous steps (curation, corpus...)
Links to Exploration step
CRIN:kucherov04aLe document en format XML
<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en" wicri:score="5">Multi-seed lossless filtration</title></titleStmt><publicationStmt><idno type="RBID">CRIN:kucherov04a</idno><date when="2004" year="2004">2004</date><idno type="wicri:Area/Crin/Corpus">003F00</idno><idno type="wicri:Area/Crin/Curation">003F00</idno><idno type="wicri:explorRef" wicri:stream="Crin" wicri:step="Curation">003F00</idno><idno type="wicri:Area/Crin/Checkpoint">000666</idno><idno type="wicri:explorRef" wicri:stream="Crin" wicri:step="Checkpoint">000666</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en">Multi-seed lossless filtration</title><author><name sortKey="Kucherov, Gregory" sort="Kucherov, Gregory" uniqKey="Kucherov G" first="Gregory" last="Kucherov">Gregory Kucherov</name></author><author><name sortKey="Noe, Laurent" sort="Noe, Laurent" uniqKey="Noe L" first="Laurent" last="Noé">Laurent Noé</name></author><author><name sortKey="Roytberg, Mikhail" sort="Roytberg, Mikhail" uniqKey="Roytberg M" first="Mikhail" last="Roytberg">Mikhail Roytberg</name></author></analytic></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>est</term><term>filtration</term><term>lossless filtering</term><term>multiple seed</term><term>oligonucleotide design</term><term>pattern matching</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en" wicri:score="610">We study a method of seed-based lossless filtration for approximate string matching and related applications. The method is based on a simultaneous use of several spaced seeds rather than a single seed as studied by Burkhardt and Karkkainen. We present algorithms to compute several important parameters of seed families, study their combinatorial properties, and describe several techniques to construct efficient families. We also report a large-scale application of the proposed technique to the problem of oligonucleotide selection for an EST sequence database.</div></front></TEI><BibTex type="inproceedings"><ref>kucherov04a</ref><crinnumber>A04-R-201</crinnumber><category>3</category><equipe>ADAGE</equipe><author><e>Kucherov, Gregory</e><e>Noé, Laurent</e><e>Roytberg, Mikhail</e></author><title>Multi-seed lossless filtration</title><booktitle>{Proceedings of the 15th Annual Symposium on Combinatorial Pattern Matching - CPM'2004, Istanbul, Turkey}</booktitle><year>2004</year><editor>Suleyman Cenk Sahinalp and S. Muthukrishnan and Ugur Dogrusoz</editor><volume>3109</volume><series>Lecture notes in computer science</series><pages>297-310</pages><month>Jul</month><publisher>Springer</publisher><keywords><e>multiple seed</e><e>lossless filtering</e><e>filtration</e><e>pattern matching</e><e>oligonucleotide design</e><e>est</e></keywords><abstract>We study a method of seed-based lossless filtration for approximate string matching and related applications. The method is based on a simultaneous use of several spaced seeds rather than a single seed as studied by Burkhardt and Karkkainen. We present algorithms to compute several important parameters of seed families, study their combinatorial properties, and describe several techniques to construct efficient families. We also report a large-scale application of the proposed technique to the problem of oligonucleotide selection for an EST sequence database.</abstract></BibTex></record>Pour manipuler ce document sous Unix (Dilib)
EXPLOR_STEP=$WICRI_ROOT/Wicri/Lorraine/explor/InforLorV4/Data/Crin/Checkpoint
HfdSelect -h $EXPLOR_STEP/biblio.hfd -nk 000666 | SxmlIndent | more
Ou
HfdSelect -h $EXPLOR_AREA/Data/Crin/Checkpoint/biblio.hfd -nk 000666 | SxmlIndent | more
Pour mettre un lien sur cette page dans le réseau Wicri
{{Explor lien
|wiki= Wicri/Lorraine
|area= InforLorV4
|flux= Crin
|étape= Checkpoint
|type= RBID
|clé= CRIN:kucherov04a
|texte= Multi-seed lossless filtration
}}
| This area was generated with Dilib version V0.6.33. |  |