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Conference Paper: AC-DIAMOND: accelerating protein alignment via better SIMD parallelization and space-efficient indexing

TitleAC-DIAMOND: accelerating protein alignment via better SIMD parallelization and space-efficient indexing
Authors
KeywordsDNA-protein alignment
SIMD
Dynamic programming
Compressed indexing
Issue Date2016
PublisherSpringer Verlag. The Journal's web site is located at http://springerlink.com/content/105633/
Citation
The 4th International Work-Conference on Bioinformatics and Biomedical Engineering (IWBBIO 2016), Granada, Spain, 20-22 April 2016. In Lecture Notes in Computer Science, 2016, v. 9656, p. 426-433 How to Cite?
AbstractTo speed up the alignment of DNA reads or assembled contigs against a protein database has been a challenge up to now. The recent tool DIAMOND has significantly improved the speed of BLASTX and RAPSearch, while giving similar degree of sensitivity. Yet for applications like metagenomics, where large amount of data is involved, DIAMOND still takes a lot of time. This paper introduces an even faster protein alignment tool, called AC-DIAMOND, which attempts to speed up DIAMOND via better SIMD parallelization and more space-efficient indexing of the reference database; the latter allows more queries to be loaded into the memory and processed together. Experimental results show that AC-DIAMOND is about 4 times faster than DIAMOND on aligning DNA reads or contigs, while retaining the same sensitivity as DIAMOND.For example, the latest assembly of the Iowa praire soil metagenomic dataset generates over 9 milllion of contigs, with a total size about 7 Gbp; when aligning these contigs to the protein database NCBI-nr, DIAMOND takes 4 to 5 days, and AC-DIAMOND takes about 1 day. AC-DIAMOND is available for testing at http://​ac-diamond.​sourceforge.​net.
DescriptionLecture Notes in Computer Science v. 9656 entitled: Bioinformatics and Biomedical Engineering: 4th International Conference, IWBBIO 2016, Granada, Spain, April 20-22, 2016, Proceedings
Persistent Identifierhttp://hdl.handle.net/10722/229703
ISBN
ISSN
2005 Impact Factor: 0.402
2015 SCImago Journal Rankings: 0.252

 

DC FieldValueLanguage
dc.contributor.authorMai, H-
dc.contributor.authorLi, D-
dc.contributor.authorZhang, Y-
dc.contributor.authorLeung, HCM-
dc.contributor.authorLuo, R-
dc.contributor.authorTing, HF-
dc.contributor.authorLam, TW-
dc.date.accessioned2016-08-23T14:12:46Z-
dc.date.available2016-08-23T14:12:46Z-
dc.date.issued2016-
dc.identifier.citationThe 4th International Work-Conference on Bioinformatics and Biomedical Engineering (IWBBIO 2016), Granada, Spain, 20-22 April 2016. In Lecture Notes in Computer Science, 2016, v. 9656, p. 426-433-
dc.identifier.isbn978-3-319-31743-4-
dc.identifier.issn0302-9743-
dc.identifier.urihttp://hdl.handle.net/10722/229703-
dc.descriptionLecture Notes in Computer Science v. 9656 entitled: Bioinformatics and Biomedical Engineering: 4th International Conference, IWBBIO 2016, Granada, Spain, April 20-22, 2016, Proceedings-
dc.description.abstractTo speed up the alignment of DNA reads or assembled contigs against a protein database has been a challenge up to now. The recent tool DIAMOND has significantly improved the speed of BLASTX and RAPSearch, while giving similar degree of sensitivity. Yet for applications like metagenomics, where large amount of data is involved, DIAMOND still takes a lot of time. This paper introduces an even faster protein alignment tool, called AC-DIAMOND, which attempts to speed up DIAMOND via better SIMD parallelization and more space-efficient indexing of the reference database; the latter allows more queries to be loaded into the memory and processed together. Experimental results show that AC-DIAMOND is about 4 times faster than DIAMOND on aligning DNA reads or contigs, while retaining the same sensitivity as DIAMOND.For example, the latest assembly of the Iowa praire soil metagenomic dataset generates over 9 milllion of contigs, with a total size about 7 Gbp; when aligning these contigs to the protein database NCBI-nr, DIAMOND takes 4 to 5 days, and AC-DIAMOND takes about 1 day. AC-DIAMOND is available for testing at http://​ac-diamond.​sourceforge.​net.-
dc.languageeng-
dc.publisherSpringer Verlag. The Journal's web site is located at http://springerlink.com/content/105633/-
dc.relation.ispartofLecture Notes in Computer Science-
dc.rightsThe final publication is available at Springer via http://dx.doi.org/[insert DOI]-
dc.subjectDNA-protein alignment-
dc.subjectSIMD-
dc.subjectDynamic programming-
dc.subjectCompressed indexing-
dc.titleAC-DIAMOND: accelerating protein alignment via better SIMD parallelization and space-efficient indexing-
dc.typeConference_Paper-
dc.identifier.emailZhang, Y: yzhang@cs.hku.hk-
dc.identifier.emailLeung, HCM: cmleung2@cs.hku.hk-
dc.identifier.emailLuo, R: rbluo@hku.hk-
dc.identifier.emailTing, HF: hfting@cs.hku.hk-
dc.identifier.emailLam, TW: twlam@cs.hku.hk-
dc.identifier.authorityLeung, HCM=rp00144-
dc.identifier.authorityTing, HF=rp00177-
dc.identifier.authorityLam, TW=rp00135-
dc.description.natureLink_to_subscribed_fulltext-
dc.identifier.doi10.1007/978-3-319-31744-1_38-
dc.identifier.scopuseid_2-s2.0-84973872479-
dc.identifier.hkuros260187-
dc.identifier.volume9656-
dc.identifier.spage426-
dc.identifier.epage433-
dc.publisher.placeGermany-
dc.customcontrol.immutablesml 160831-

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