Deutsch
 
Hilfe Datenschutzhinweis Impressum
  DetailsucheBrowse

Datensatz

 
 
DownloadE-Mail
  q-gram Based Database Searching Using a Suffix Array (QUASAR)

Burkhardt, S., Crauser, A., Ferragina, P., Lenhof, H.-P., Rivals, E., & Vingron, M. (1999). q-gram Based Database Searching Using a Suffix Array (QUASAR). In S. Istrail, P. Pevzner, & M. Waterman (Eds.), Proceedings of the 3rd Annual International Conference on Computational Molecular Biology (RECOMB-99) (pp. 77-83). New York, USA: ACM.

Item is

Externe Referenzen

einblenden:

Urheber

einblenden:
ausblenden:
 Urheber:
Burkhardt, Stefan1, Autor           
Crauser, Andreas1, Autor           
Ferragina, Paolo1, Autor           
Lenhof, Hans-Peter1, Autor           
Rivals, Eric1, Autor           
Vingron, Martin, Autor
Affiliations:
1Algorithms and Complexity, MPI for Informatics, Max Planck Society, ou_24019              

Inhalt

einblenden:
ausblenden:
Schlagwörter: -
 Zusammenfassung: With the increasing amount of DNA sequence information deposited in our databases searching for similarity to a query sequence has become a basic operation in molecular biology. But even todays fast algorithms reach their limits when applied to all-versus-all comparisons of large databases. Here we present a new data base searching algorithm dubbed QUASAR (Q-gram Alignment based on Suffix ARrays) which was designed to quickly detect sequences with strong similarity to the query in a context where many searches are conducted on one database. Our algorithm applies a modification of $q$-tuple filtering implemented on top of a suffix array. Two versions were developed, one for a RAM resident suffix array and one for access to the suffix array on disk. We compared our implementation with BLAST and found that our approach is an order of magnitude faster. It is, however, restricted to the search for strongly similar DNA sequences as is typically required, e.g., in the context of clustering expressed sequence tags (ESTs).

Details

einblenden:
ausblenden:
Sprache(n): eng - English
 Datum: 2010-03-021999
 Publikationsstatus: Erschienen
 Seiten: -
 Ort, Verlag, Ausgabe: New York, USA : ACM
 Inhaltsverzeichnis: -
 Art der Begutachtung: -
 Identifikatoren: eDoc: 518074
Anderer: Local-ID: C1256428004B93B8-5611988C44151F5CC12568B200520F68-Burkhardt1999/1
 Art des Abschluß: -

Veranstaltung

einblenden:
ausblenden:
Titel: Untitled Event
Veranstaltungsort: Lyon, France
Start-/Enddatum: 1999

Entscheidung

einblenden:

Projektinformation

einblenden:

Quelle 1

einblenden:
ausblenden:
Titel: Proceedings of the 3rd Annual International Conference on Computational Molecular Biology (RECOMB-99)
Genre der Quelle: Konferenzband
 Urheber:
Istrail, Sorin, Herausgeber
Pevzner, Pavel, Herausgeber
Waterman, Michael, Herausgeber
Affiliations:
-
Ort, Verlag, Ausgabe: New York, USA : ACM
Seiten: - Band / Heft: - Artikelnummer: - Start- / Endseite: 77 - 83 Identifikator: ISBN: 1-58113-069-4