메뉴 건너뛰기




Volumn 5724 LNBI, Issue , 2009, Pages 246-260

Mpscan: Fast localisation of multiple reads in genomes

Author keywords

[No Author keywords available]

Indexed keywords

BOW TIE; DESKTOP COMPUTER; EXACT MATCHING; LOCALISATION; LOW MEMORY; MAPPING APPLICATIONS; SHORT SEQUENCES; SINGLE PASS; SUBLINEAR; TEXT LENGTH; TIME COMPLEXITY;

EID: 70350361065     PISSN: 03029743     EISSN: 16113349     Source Type: Book Series    
DOI: 10.1007/978-3-642-04241-6_21     Document Type: Conference Paper
Times cited : (18)

References (27)
  • 1
    • 34250201129 scopus 로고    scopus 로고
    • Polony Multiplex Analysis of Gene Expression (PMAGE) in Mouse Hypertrophic Cardiomyopathy
    • Kim, J., Porreca, G., Song, L., Greenway, S., Gorham, J., Church, G., Seidman, C., Seidman, J.: Polony Multiplex Analysis of Gene Expression (PMAGE) in Mouse Hypertrophic Cardiomyopathy. Science 316 (5830), 1481-1484 (2007)
    • (2007) Science , vol.316 , Issue.5830 , pp. 1481-1484
    • Kim, J.1    Porreca, G.2    Song, L.3    Greenway, S.4    Gorham, J.5    Church, G.6    Seidman, C.7    Seidman, J.8
  • 2
    • 34250159524 scopus 로고    scopus 로고
    • Genome-Wide Mapping of in Vivo Protein-DNA Interactions
    • Johnson, D., Mortazavi, A., Myers, R., Wold, B.: Genome-Wide Mapping of in Vivo Protein-DNA Interactions. Science 316 (5830), 1497-1502 (2007)
    • (2007) Science , vol.316 , Issue.5830 , pp. 1497-1502
    • Johnson, D.1    Mortazavi, A.2    Myers, R.3    Wold, B.4
  • 4
    • 39449088572 scopus 로고    scopus 로고
    • Genome-wide approaches to studying chromatin modifications
    • Schones, D., Zhao, K.: Genome-wide approaches to studying chromatin modifications. Nat. Rev. Genet. 9(3), 179-191 (2008)
    • (2008) Nat. Rev. Genet , vol.9 , Issue.3 , pp. 179-191
    • Schones, D.1    Zhao, K.2
  • 5
    • 34547630151 scopus 로고    scopus 로고
    • ChIP-seq: Welcome to the new frontier
    • Mardis, E.R.: ChIP-seq: welcome to the new frontier. Nat. Methods 4(8), 613-614 (2007)
    • (2007) Nat. Methods , vol.4 , Issue.8 , pp. 613-614
    • Mardis, E.R.1
  • 9
    • 55549097836 scopus 로고    scopus 로고
    • Li, H., Ruan, J., Durbin, R.: Mapping short DNA sequencing reads and calling variants using mapping quality scores. Genome Res. 18, 1851-1858 (2008) (in press)
    • Li, H., Ruan, J., Durbin, R.: Mapping short DNA sequencing reads and calling variants using mapping quality scores. Genome Res. 18, 1851-1858 (2008) (in press)
  • 10
    • 40049104732 scopus 로고    scopus 로고
    • SOAP: Short oligonucleotide alignment program
    • Li, R., Li, Y., Kristiansen, K., Wang, J.: SOAP: short oligonucleotide alignment program. Bioinformatics 24(5), 713-714 (2008)
    • (2008) Bioinformatics , vol.24 , Issue.5 , pp. 713-714
    • Li, R.1    Li, Y.2    Kristiansen, K.3    Wang, J.4
  • 11
    • 41249096306 scopus 로고    scopus 로고
    • Using quality scores and longer reads improves accuracy of solexa read mapping
    • Smith, A., Xuan, Z., Zhang, M.: Using quality scores and longer reads improves accuracy of solexa read mapping. BMC Bioinformatics 9(1), 128 (2008)
    • (2008) BMC Bioinformatics , vol.9 , Issue.1 , pp. 128
    • Smith, A.1    Xuan, Z.2    Zhang, M.3
  • 12
    • 62349130698 scopus 로고    scopus 로고
    • Ultrafast and memory-efficient alignment of short dna sequences to the human genome
    • Langmead, B., Trapnell, C., Pop, M., Salzberg, S.: Ultrafast and memory-efficient alignment of short dna sequences to the human genome. Genome Biology 10(3), R25 (2009)
    • (2009) Genome Biology , vol.10 , Issue.3
    • Langmead, B.1    Trapnell, C.2    Pop, M.3    Salzberg, S.4
  • 13
    • 53749083993 scopus 로고    scopus 로고
    • Seqmap: Mapping massive amount of oligonucleotides to the genome
    • Jiang, H., Wong, W.H.: Seqmap: mapping massive amount of oligonucleotides to the genome. Bioinformatics 24(20), 2395-2396 (2008)
    • (2008) Bioinformatics , vol.24 , Issue.20 , pp. 2395-2396
    • Jiang, H.1    Wong, W.H.2
  • 16
    • 0036226603 scopus 로고    scopus 로고
    • BLAT - The BLAST-Like Alignment Tool
    • Kent, J.W.: BLAT - The BLAST-Like Alignment Tool. Genome Res. 12(4), 656-664 (2002)
    • (2002) Genome Res , vol.12 , Issue.4 , pp. 656-664
    • Kent, J.W.1
  • 18
    • 0034764307 scopus 로고    scopus 로고
    • Ning, Z., Cox, A., Mulikin, J.: SSAHA: A Fast Search Method for large DNA Databases. Genome Res. 11, 1725-1729 (2001)
    • Ning, Z., Cox, A., Mulikin, J.: SSAHA: A Fast Search Method for large DNA Databases. Genome Res. 11, 1725-1729 (2001)
  • 19
    • 39349104728 scopus 로고    scopus 로고
    • Indexing Strategies for Rapid Searches of Short Words in Genome Sequences
    • Iseli, C., Ambrosini, G., Bucher, P., Jongeneel, C.: Indexing Strategies for Rapid Searches of Short Words in Genome Sequences. PLoS ONE 2(6), e579 (2007)
    • (2007) PLoS ONE , vol.2 , Issue.6
    • Iseli, C.1    Ambrosini, G.2    Bucher, P.3    Jongeneel, C.4
  • 20
    • 54949110994 scopus 로고    scopus 로고
    • ZOOM! Zillions of oligos mapped
    • Lin, H., Zhang, Z., Zhang, M.Q., Ma, B., Li, M.: ZOOM! Zillions of oligos mapped. Bioinformatics 24(21), 2431-2437 (2008)
    • (2008) Bioinformatics , vol.24 , Issue.21 , pp. 2431-2437
    • Lin, H.1    Zhang, Z.2    Zhang, M.Q.3    Ma, B.4    Li, M.5
  • 21
    • 57449100870 scopus 로고    scopus 로고
    • Design and analysis of ChIP-seq experiments for DNA-binding proteins
    • Kharchenko, P., Tolstorukov, M.Y., Park, P.J.: Design and analysis of ChIP-seq experiments for DNA-binding proteins. Nat. Biotech. 26(12), 1351-1359 (2008)
    • (2008) Nat. Biotech , vol.26 , Issue.12 , pp. 1351-1359
    • Kharchenko, P.1    Tolstorukov, M.Y.2    Park, P.J.3
  • 23
    • 3242675870 scopus 로고    scopus 로고
    • Average complexity of exact and approximate multiple string matching
    • Navarro, G., Fredriksson, K.: Average complexity of exact and approximate multiple string matching. Theoretical Computer Science 321(2-3), 283-290 (2004)
    • (2004) Theoretical Computer Science , vol.321 , Issue.2-3 , pp. 283-290
    • Navarro, G.1    Fredriksson, K.2
  • 24
    • 39149083734 scopus 로고    scopus 로고
    • A rescue strategy for multimapping short sequence tags refines surveys of transcriptional activity by CAGE
    • Faulkner, G., Forrest, A., Chalk, A., Schroder, K., Hayashizaki, Y., Carninci, P., Hume, D., Grimmond, S.: A rescue strategy for multimapping short sequence tags refines surveys of transcriptional activity by CAGE. Genomics 91, 281-288 (2008)
    • (2008) Genomics , vol.91 , pp. 281-288
    • Faulkner, G.1    Forrest, A.2    Chalk, A.3    Schroder, K.4    Hayashizaki, Y.5    Carninci, P.6    Hume, D.7    Grimmond, S.8
  • 26
    • 34547105834 scopus 로고    scopus 로고
    • On the complexity of the spaced seeds
    • Ma, B., Li, M.: On the complexity of the spaced seeds. J. of Computer and System Sciences 73(7), 1024-1034 (2007)
    • (2007) J. of Computer and System Sciences , vol.73 , Issue.7 , pp. 1024-1034
    • Ma, B.1    Li, M.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.