Please use this identifier to cite or link to this item: https://hdl.handle.net/20.500.11851/1150
Full metadata record
DC FieldValueLanguage
dc.contributor.authorAlser, Mohammed-
dc.contributor.authorHassan, Hasan-
dc.contributor.authorXin, Hongyi-
dc.contributor.authorErgin, Oğuz-
dc.contributor.authorMutlu, Onur-
dc.contributor.authorAlkan, Can-
dc.date.accessioned2019-06-26T07:40:34Z-
dc.date.available2019-06-26T07:40:34Z-
dc.date.issued2017-11-01-
dc.identifier.citationAlser, M., Hassan, H., Xin, H., Ergin, O., Mutlu, O., & Alkan, C. (2017). GateKeeper: a new hardware architecture for accelerating pre-alignment in DNA short read mapping. Bioinformatics, 33(21), 3355-3363.en_US
dc.identifier.issn1367-4803-
dc.identifier.urihttps://academic.oup.com/bioinformatics/article/33/21/3355/3859176-
dc.identifier.urihttps://hdl.handle.net/20.500.11851/1150-
dc.description.abstractMotivation: High throughput DNA sequencing (HTS) technologies generate an excessive number of small DNA segments - called short reads- that cause significant computational burden. To analyze the entire genome, each of the billions of short reads must be mapped to a reference genome based on the similarity between a read and 'candidate' locations in that reference genome. The similarity measurement, called alignment, formulated as an approximate string matching problem, is the computational bottleneck because: (i) it is implemented using quadratic-time dynamic programming algorithms and (ii) the majority of candidate locations in the reference genome do not align with a given read due to high dissimilarity. Calculating the alignment of such incorrect candidate locations consumes an overwhelming majority of a modern read mapper's execution time. Therefore, it is crucial to develop a fast and effective filter that can detect incorrect candidate locations and eliminate them before invoking computationally costly alignment algorithms. Results: We propose GateKeeper, a new hardware accelerator that functions as a pre-alignment step that quickly filters out most incorrect candidate locations. GateKeeper is the first design to accelerate pre-alignment using Field-Programmable Gate Arrays (FPGAs), which can perform pre-alignment much faster than software. When implemented on a single FPGA chip, GateKeeper maintains high accuracy (on average >96%) while providing, on average, 90-fold and 130-fold speedup over the state-of-the-art software pre-alignment techniques, Adjacency Filter and Shifted Hamming Distance (SHD), respectively. The addition of GateKeeper as a pre-alignment step can reduce the verification time of the mrFAST mapper by a factor of 10.en_US
dc.language.isoenen_US
dc.publisherOxford Univ Pressen_US
dc.relation.ispartofBioinformaticsen_US
dc.rightsinfo:eu-repo/semantics/openAccessen_US
dc.subjectGenomeen_US
dc.subjectExomeen_US
dc.subjectread mappingen_US
dc.titleGatekeeper: a New Hardware Architecture for Accelerating Pre-Alignment in Dna Short Read Mappingen_US
dc.typeArticleen_US
dc.departmentFaculties, Faculty of Engineering, Department of Computer Engineeringen_US
dc.departmentFakülteler, Mühendislik Fakültesi, Bilgisayar Mühendisliği Bölümütr_TR
dc.identifier.volume33-
dc.identifier.issue21-
dc.identifier.startpage3355-
dc.identifier.endpage3363-
dc.relation.tubitakScientific and Technological Research Council of Turkey, under the TUBITAK 2215 programen_US
dc.relation.ecMarie Curie Career Integration Grant [PCIG-2011-303772]-
dc.authorid0000-0003-2701-3787-
dc.identifier.wosWOS:000413645800004en_US
dc.identifier.scopus2-s2.0-85034098310en_US
dc.institutionauthorErgin, Oğuz-
dc.identifier.pmid28575161en_US
dc.identifier.doi10.1093/bioinformatics/btx342-
dc.authorwosidE-5717-2010-
dc.authorscopusid6603141208-
dc.relation.publicationcategoryMakale - Uluslararası Hakemli Dergi - Kurum Öğretim Elemanıen_US
dc.relation.otherNIH [R01 HG006004]en_US
dc.identifier.scopusqualityQ1-
item.openairetypeArticle-
item.languageiso639-1en-
item.grantfulltextopen-
item.fulltextWith Fulltext-
item.openairecristypehttp://purl.org/coar/resource_type/c_18cf-
item.cerifentitytypePublications-
crisitem.author.dept02.3. Department of Computer Engineering-
Appears in Collections:Bilgisayar Mühendisliği Bölümü / Department of Computer Engineering
PubMed İndeksli Yayınlar Koleksiyonu / PubMed Indexed Publications Collection
Scopus İndeksli Yayınlar Koleksiyonu / Scopus Indexed Publications Collection
WoS İndeksli Yayınlar Koleksiyonu / WoS Indexed Publications Collection
Files in This Item:
File SizeFormat 
1150.pdf566.5 kBAdobe PDFView/Open
Show simple item record



CORE Recommender

SCOPUSTM   
Citations

35
checked on Dec 21, 2024

WEB OF SCIENCETM
Citations

61
checked on Oct 5, 2024

Page view(s)

212
checked on Dec 23, 2024

Google ScholarTM

Check




Altmetric


Items in GCRIS Repository are protected by copyright, with all rights reserved, unless otherwise indicated.