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Pregled bibliografske jedinice broj: 643444

SW#–GPU-enabled exact alignments on genome scale


Korpar, Matija; Šikić, Mile
SW#–GPU-enabled exact alignments on genome scale // Bioinformatics, 29 (2013), 19; 2494-2495 doi:10.1093/bioinformatics/btt410 (međunarodna recenzija, kratko priopcenje, znanstveni)


CROSBI ID: 643444 Za ispravke kontaktirajte CROSBI podršku putem web obrasca

Naslov
SW#–GPU-enabled exact alignments on genome scale

Autori
Korpar, Matija ; Šikić, Mile

Izvornik
Bioinformatics (1367-4803) 29 (2013), 19; 2494-2495

Vrsta, podvrsta i kategorija rada
Radovi u časopisima, kratko priopcenje, znanstveni

Ključne riječi
sequence alignment; algorithm; Smith-Waterman; GPU

Sažetak
We propose SW#, a new CUDA graphical processor unit-enabled and memory-efficient implementation of dynamic programming algorithm, for local alignment. It can be used as either a stand-alone application or a library. Although there are other graphical processor unit implementations of the Smith–Waterman algorithm, SW# is the only one publicly available that can produce sequence alignments on genome-wide scale. For long sequences, it is at least a few hundred times faster than a CPU version of the same algorithm.

Izvorni jezik
Engleski

Znanstvena područja
Računarstvo



POVEZANOST RADA


Projekti:
036-0362214-1987 - Modeliranje kompleksnih sustava (Jeren, Branko, MZOS ) ( POIROT)

Ustanove:
Fakultet elektrotehnike i računarstva, Zagreb

Profili:

Avatar Url Mile Šikić (autor)

Citiraj ovu publikaciju

Korpar, Matija; Šikić, Mile
SW#–GPU-enabled exact alignments on genome scale // Bioinformatics, 29 (2013), 19; 2494-2495 doi:10.1093/bioinformatics/btt410 (međunarodna recenzija, kratko priopcenje, znanstveni)
Korpar, M. & Šikić, M. (2013) SW#–GPU-enabled exact alignments on genome scale. Bioinformatics, 29 (19), 2494-2495 doi:10.1093/bioinformatics/btt410.
@article{article, year = {2013}, pages = {2494-2495}, DOI = {10.1093/bioinformatics/btt410}, keywords = {sequence alignment, algorithm, Smith-Waterman, GPU}, journal = {Bioinformatics}, doi = {10.1093/bioinformatics/btt410}, volume = {29}, number = {19}, issn = {1367-4803}, title = {SW\#–GPU-enabled exact alignments on genome scale}, keyword = {sequence alignment, algorithm, Smith-Waterman, GPU} }
@article{article, year = {2013}, pages = {2494-2495}, DOI = {10.1093/bioinformatics/btt410}, keywords = {sequence alignment, algorithm, Smith-Waterman, GPU}, journal = {Bioinformatics}, doi = {10.1093/bioinformatics/btt410}, volume = {29}, number = {19}, issn = {1367-4803}, title = {SW\#–GPU-enabled exact alignments on genome scale}, keyword = {sequence alignment, algorithm, Smith-Waterman, GPU} }

Časopis indeksira:


  • Current Contents Connect (CCC)
  • Web of Science Core Collection (WoSCC)
    • Science Citation Index Expanded (SCI-EXP)
    • SCI-EXP, SSCI i/ili A&HCI
  • Scopus
  • MEDLINE


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