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Volumn 8, Issue 12, 2013, Pages

SSW library: An SIMD Smith-Waterman C/C++ library for use in genomic applications

Author keywords

[No Author keywords available]

Indexed keywords

AMINO ACID SEQUENCE; ARTICLE; BACTERIAL GENOME; COMPUTER LANGUAGE; COMPUTER PROGRAM; CONTROLLED STUDY; ESCHERICHIA COLI; GENE SEQUENCE; GENETIC ALGORITHM; HUMAN; HUMAN GENOME; NONHUMAN; NUCLEOTIDE SEQUENCE; SARS CORONAVIRUS; SEQUENCE ALIGNMENT; TOXOPLASMA GONDII; VIRUS GENOME;

EID: 84891755297     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0082138     Document Type: Article
Times cited : (164)

References (16)
  • 1
    • 0019887799 scopus 로고
    • Identification of common molecular subsequences
    • doi: 10.1016/0022-2836(81)90087-5. PubMed: 7265238
    • Smith TF, Waterman MS (1981) Identification of common molecular subsequences. J Mol Biol 147: 195-197. doi: 10.1016/0022-2836(81)90087-5. PubMed: 7265238.
    • (1981) J Mol Biol , vol.147 , pp. 195-197
    • Smith, T.F.1    Waterman, M.S.2
  • 2
    • 0020484488 scopus 로고
    • An improved algorithm for matching biological sequences
    • doi: 10.1016/0022-2836(82)90398-9. PubMed: 7166760
    • Gotoh O (1982) An improved algorithm for matching biological sequences. J Mol Biol 162(3): 705-708. doi: 10.1016/0022-2836(82)90398-9. PubMed: 7166760.
    • (1982) J Mol Biol , vol.162 , Issue.3 , pp. 705-708
    • Gotoh, O.1
  • 4
    • 77951106340 scopus 로고    scopus 로고
    • CUDASW++2.0: Enhanced Smith-Waterman protein database search on CUDA-enabled GPUs based on SIMT and virtualized SIMD abstractions
    • doi: 10.1186/1756-0500-3-93. PubMed: 20370891
    • Liu Y, Schmidt B, Maskell DL (2010) CUDASW++2.0: enhanced Smith-Waterman protein database search on CUDA-enabled GPUs based on SIMT and virtualized SIMD abstractions. BMC Res Notes 3: 93. doi: 10.1186/1756-0500-3-93. PubMed: 20370891.
    • (2010) BMC Res Notes , vol.3 , pp. 93
    • Liu, Y.1    Schmidt, B.2    Maskell, D.L.3
  • 5
    • 84875688710 scopus 로고    scopus 로고
    • CUDASW++ 3.0: Accelerating Smith-Waterman protein database search by coupling CPU and GPU SIMD instructions
    • doi: 10.1186/1471-2105-14-117. PubMed: 23557111
    • Liu Y, Wirawan A, Schmidt B (2013) CUDASW++ 3.0: accelerating Smith-Waterman protein database search by coupling CPU and GPU SIMD instructions. BMC Bioinformatics 14: 117. doi: 10.1186/1471-2105-14-117. PubMed: 23557111.
    • (2013) BMC Bioinformatics , vol.14 , pp. 117
    • Liu, Y.1    Wirawan, A.2    Schmidt, B.3
  • 6
    • 84891762289 scopus 로고    scopus 로고
    • SW#-GPU-enabled exact alignments on genome scale
    • doi:10.1093/ bioinformatics/btt410. PubMed: 23864730
    • Korpar M, Šikic M (2013) SW#-GPU-enabled exact alignments on genome scale. Bioinformatics 29: 2494-2495. doi:10.1093/ bioinformatics/btt410. PubMed: 23864730.
    • (2013) Bioinformatics , vol.29 , pp. 2494-2495
    • Korpar, M.1    Šikic, M.2
  • 7
    • 0030935244 scopus 로고    scopus 로고
    • Using video-oriented instructions to speed up sequence comparison
    • PubMed: 9146961
    • Wozniak A (1997) Using video-oriented instructions to speed up sequence comparison. Comput Appl Biosci 13(2): 145-150. PubMed: 9146961.
    • (1997) Comput Appl Biosci , vol.13 , Issue.2 , pp. 145-150
    • Wozniak, A.1
  • 8
    • 79957630864 scopus 로고    scopus 로고
    • Faster Smith-Waterman database searches with inter-sequence SIMD parallelisation
    • doi: 10.1186/1471-2105-12-221. PubMed: 21631914
    • Rognes T (2011) Faster Smith-Waterman database searches with inter-sequence SIMD parallelisation. BMC Bioinformatics 12: 221. doi: 10.1186/1471-2105-12-221. PubMed: 21631914.
    • (2011) BMC Bioinformatics , vol.12 , pp. 221
    • Rognes, T.1
  • 9
    • 33846697176 scopus 로고    scopus 로고
    • Striped Smith-Waterman speeds database searches six times over other SIMD implementations
    • doi:10.1093/bioinformatics/btl319. PubMed: 17110365
    • Farrar M (2007) Striped Smith-Waterman speeds database searches six times over other SIMD implementations. Bioinformatics 23(2): 156-161. doi:10.1093/bioinformatics/btl319. PubMed: 17110365.
    • (2007) Bioinformatics , vol.23 , Issue.2 , pp. 156-161
    • Farrar, M.1
  • 10
    • 77049114671 scopus 로고    scopus 로고
    • SWPS3 - Fast multi-threaded vectorized Smith-Waterman for IBM Cell/ B.E. and x86/SSE2
    • doi: 10.1186/1756-0500-1-107. PubMed: 18959793
    • Szalkowski A, Ledergerber C, Krähenbühl P, Dessimoz C (2008) SWPS3 - fast multi-threaded vectorized Smith-Waterman for IBM Cell/ B.E. and x86/SSE2. BMC Res Notes 1: 107. doi: 10.1186/1756-0500-1-107. PubMed: 18959793.
    • (2008) BMC Res Notes , vol.1 , pp. 107
    • Szalkowski, A.1    Ledergerber, C.2    Krähenbühl, P.3    Dessimoz, C.4
  • 11
    • 77949587649 scopus 로고    scopus 로고
    • Fast and accurate long-read alignment with Burrows-Wheeler transform
    • doi: 10.1093/bioinformatics/btp698. PubMed: 20080505
    • Li H, Durbin R (2010) Fast and accurate long-read alignment with Burrows-Wheeler transform. Bioinformatics 26(5): 589-595. doi: 10.1093/bioinformatics/btp698. PubMed: 20080505.
    • (2010) Bioinformatics , vol.26 , Issue.5 , pp. 589-595
    • Li, H.1    Durbin, R.2
  • 12
    • 84859210032 scopus 로고    scopus 로고
    • Fast gapped-read alignment with Bowtie 2
    • doi:10.1038/nmeth.1923. PubMed: 22388286
    • Langmead B, Salzberg SL (2012) Fast gapped-read alignment with Bowtie 2. Nat Methods 9(4): 357-359. doi:10.1038/nmeth.1923. PubMed: 22388286.
    • (2012) Nat Methods , vol.9 , Issue.4 , pp. 357-359
    • Langmead, B.1    Salzberg, S.L.2
  • 13
    • 79956307251 scopus 로고    scopus 로고
    • Stampy: A statistical algorithm for sensitive and fast mapping of Illumina sequence reads
    • doi:10.1101/gr.111120.110. PubMed: 20980556
    • Lunter G, Goodson M (2011) Stampy: a statistical algorithm for sensitive and fast mapping of Illumina sequence reads. Genome Res 21(6): 936-939. doi:10.1101/gr.111120.110. PubMed: 20980556.
    • (2011) Genome Res , vol.21 , Issue.6 , pp. 936-939
    • Lunter, G.1    Goodson, M.2
  • 15
    • 84975742565 scopus 로고    scopus 로고
    • A map of human genome variation from population-scale sequencing
    • 1000 Genomes Project Consortium
    • 1000 Genomes Project Consortium, Abecasis GR, Altshuler D, Auton A, Brooks LD, et al. (2010) A map of human genome variation from population-scale sequencing. Nature 467(7319):1061-73
    • (2010) Nature , vol.467 , Issue.7319 , pp. 1061-1073
    • Abecasis, G.R.1    Altshuler, D.2    Auton, A.3    Brooks, L.D.4
  • 16
    • 84975795680 scopus 로고    scopus 로고
    • An integrated map of genetic variation from 1,092 human genomes
    • 1000 Genomes Project Consortium
    • 1000 Genomes Project Consortium, Abecasis GR, Auton A, Brooks LD, DePristo MA, et al. (2012). An integrated map of genetic variation from 1,092 human genomes. Nature 491(7422):56-65
    • (2012) Nature , vol.491 , Issue.7422 , pp. 56-65
    • Abecasis, G.R.1    Auton, A.2    Brooks, L.D.3    DePristo, M.A.4


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.