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Volumn 28, Issue 18, 2012, Pages

Indel-tolerant read mapping with trinucleotide frequencies using cache-oblivious kd-trees

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NUCLEOTIDE;

EID: 84866463002     PISSN: 13674803     EISSN: 14602059     Source Type: Journal    
DOI: 10.1093/bioinformatics/bts380     Document Type: Article
Times cited : (3)

References (57)
  • 2
    • 70349556543 scopus 로고    scopus 로고
    • Personalized copy number and segmental duplication maps using next-generation sequencing
    • Alkan,C. et al. (2009) Personalized copy number and segmental duplication maps using next-generation sequencing. Nat. Genet., 41, 1061-1067.
    • (2009) Nat. Genet. , vol.41 , pp. 1061-1067
    • Alkan, C.1
  • 3
    • 79954672317 scopus 로고    scopus 로고
    • Genome structural variation discovery and genotyping
    • Alkan,C. et al. (2011) Genome structural variation discovery and genotyping. Nat. Rev. Genet., 12, 363-376.
    • (2011) Nat. Rev. Genet. , vol.12 , pp. 363-376
    • Alkan, C.1
  • 4
    • 26444524649 scopus 로고    scopus 로고
    • Cache-oblivious data structures
    • Mehta,D. et al. (eds.), CRC Press, Boca Raton, chapter 34.
    • Arge,L. et al. (2005) Cache-oblivious data structures. In Mehta,D. et al. (eds.) Handbook of Data Structures and Applications, CRC Press, Boca Raton, chapter 34.
    • (2005) Handbook of Data Structures and Applications
    • Arge, L.1
  • 5
    • 0001802606 scopus 로고    scopus 로고
    • The x-tree: An index structure for high-dimensional data
    • Vijayaraman,T.M. et al. (eds), September 3-6, 1996, Mumbai, India. Morgan Kaufmann, San Francisco
    • Berchtold,S. et al. (1996) The x-tree: An index structure for high-dimensional data. In Vijayaraman,T.M. et al. (eds). VLDB'96, Proceedings of 22th International Conference on Very Large Data Bases, September 3-6, 1996, Mumbai, India. Morgan Kaufmann, San Francisco, pp. 28-39.
    • (1996) VLDB'96, Proceedings of 22th International Conference on Very Large Data Bases , pp. 28-39
    • Berchtold, S.1
  • 6
    • 0027540038 scopus 로고
    • Approximate closest-point queries in high dimensions
    • Bern,M. (1993) Approximate closest-point queries in high dimensions. Inf. Process Lett., 45, 95-99.
    • (1993) Inf. Process Lett. , vol.45 , pp. 95-99
    • Bern, M.1
  • 7
    • 0038670812 scopus 로고    scopus 로고
    • Searching in high-dimensional spaces: Index structures for improving the performance of multimedia databases
    • Böhm,C. et al. (2001) Searching in high-dimensional spaces: Index structures for improving the performance of multimedia databases. ACM Comput. Surv., 33, 322-373.
    • (2001) ACM Comput. Surv. , vol.33 , pp. 322-373
    • Böhm, C.1
  • 8
    • 84855336145 scopus 로고    scopus 로고
    • Indexing methods for approximate dictionary searching
    • Boytsov,L. (2011a) Indexing methods for approximate dictionary searching. J. Exp. Algorithmics, 16, 1.
    • (2011) J. Exp. Algorithmics , vol.16 , pp. 1
    • Boytsov, L.1
  • 9
    • 84855336145 scopus 로고    scopus 로고
    • Indexing methods for approximate dictionary searching: Comparative analysis
    • 1.1:1.1-1.1:1.91
    • Boytsov,L. (2011b) Indexing methods for approximate dictionary searching: Comparative analysis. J. Exp. Algorithmics, 16, 1.1:1.1-1.1:1.91.
    • (2011) J. Exp. Algorithmics , vol.16
    • Boytsov, L.1
  • 10
    • 84877703200 scopus 로고
    • A spatial index for approximate multiple string matching
    • Bugnion,E. et al. (1995) A spatial index for approximate multiple string matching. J. Brazilian Chem. Soc., 1, 28-35.
    • (1995) J. Brazilian Chem. Soc. , vol.1 , pp. 28-35
    • Bugnion, E.1
  • 11
    • 0141717105 scopus 로고    scopus 로고
    • Better filtering with gapped q-grams
    • Burkhardt,S. and Kärkkäinen,J. (2002) Better filtering with gapped q-grams. Fundam. Inf., 56, 51-70.
    • (2002) Fundam. Inf. , vol.56 , pp. 51-70
    • Burkhardt, S.1    Kärkkäinen, J.2
  • 12
    • 59849118874 scopus 로고    scopus 로고
    • Improving the space cost of k -nn search in metric spaces by using distance estimators
    • Bustos,B. and Navarro,G. (2009) Improving the space cost of k -nn search in metric spaces by using distance estimators. Multimedia Tools Appl., 41, 215-233.
    • (2009) Multimedia Tools Appl. , vol.41 , pp. 215-233
    • Bustos, B.1    Navarro, G.2
  • 13
    • 69549116107 scopus 로고    scopus 로고
    • Breakdancer: an algorithm for high-resolution mapping of genomic structural variation
    • Chen,K. et al. (2009) Breakdancer: an algorithm for high-resolution mapping of genomic structural variation. Nat. Methods, 6, 677-681.
    • (2009) Nat. Methods , vol.6 , pp. 677-681
    • Chen, K.1
  • 14
    • 0031978181 scopus 로고    scopus 로고
    • Base-calling of automated sequencer traces using phred. II. error probabilities
    • Ewing,B. and Green,P. (1998) Base-calling of automated sequencer traces using phred. II. error probabilities. Genome Res., 8, 186-194.
    • (1998) Genome Res. , vol.8 , pp. 186-194
    • Ewing, B.1    Green, P.2
  • 16
    • 77954139210 scopus 로고    scopus 로고
    • Incorporating sequence quality data into alignment improves DNA read mapping
    • Frith,M.C. et al. (2010) Incorporating sequence quality data into alignment improves DNA read mapping. Nucleic Acids Res., 38, e100.
    • (2010) Nucleic Acids Res. , vol.38
    • Frith, M.C.1
  • 17
    • 84857867828 scopus 로고    scopus 로고
    • Estimation of pairwise sequence similarity of mammalian enhancers with word neighbourhood counts
    • Goke,J. et al. (2012) Estimation of pairwise sequence similarity of mammalian enhancers with word neighbourhood counts. Bioinformatics, 28, 656-663.
    • (2012) Bioinformatics , vol.28 , pp. 656-663
    • Goke, J.1
  • 19
    • 77955163329 scopus 로고    scopus 로고
    • mrsfast: a cache-oblivious algorithm for short-read mapping
    • Hach,F. et al. (2010) mrsfast: a cache-oblivious algorithm for short-read mapping. Nat. Method., 7, 576-577.
    • (2010) Nat. Method. , vol.7 , pp. 576-577
    • Hach, F.1
  • 20
    • 80755171163 scopus 로고    scopus 로고
    • Probabilistic alignments with quality scores: an application to short-read mapping toward accurate snp/indel detection
    • Hamada,M. et al. (2011) Probabilistic alignments with quality scores: an application to short-read mapping toward accurate snp/indel detection. Bioinformatics, 27, 3085-3092.
    • (2011) Bioinformatics , vol.27 , pp. 3085-3092
    • Hamada, M.1
  • 21
    • 67650064593 scopus 로고    scopus 로고
    • Combinatorial algorithms for structural variation detection in high-throughput sequenced genomes
    • Hormozdiari,F. et al. (2009) Combinatorial algorithms for structural variation detection in high-throughput sequenced genomes. Genome Res., 19, 1270-1278.
    • (2009) Genome Res. , vol.19 , pp. 1270-1278
    • Hormozdiari, F.1
  • 22
    • 77954205450 scopus 로고    scopus 로고
    • Next-generation variationhunter: combinatorial algorithms for transposon insertion discovery
    • Hormozdiari,F. et al. (2010) Next-generation variationhunter: combinatorial algorithms for transposon insertion discovery. Bioinformatics, 26, i350-i357.
    • (2010) Bioinformatics , vol.26
    • Hormozdiari, F.1
  • 23
    • 28444491040 scopus 로고    scopus 로고
    • Fast approximate similarity search in extremely highdimensional data sets
    • Aberer,K. et al. (eds), Washington, DC
    • Houle,M.E. and Sakuma,J. (2005) Fast approximate similarity search in extremely highdimensional data sets. In Aberer,K. et al. (eds). ICDE. IEEE Computer Society, Washington, DC, pp. 619-630.
    • (2005) ICDE. IEEE Computer Society , pp. 619-630
    • Houle, M.E.1    Sakuma, J.2
  • 24
    • 11744325540 scopus 로고    scopus 로고
    • Sr-tree: An index structure for nearest-neighbor searching of high-dimensional point data
    • Katayama,N. and Satoh,S. (1998) Sr-tree: An index structure for nearest-neighbor searching of high-dimensional point data. Sys. Comput. Japan, 29, 59-73.
    • (1998) Sys. Comput. Japan , vol.29 , pp. 59-73
    • Katayama, N.1    Satoh, S.2
  • 26
    • 62549131646 scopus 로고    scopus 로고
    • Pemer: a computational framework with simulation-based error models for inferring genomic structural variants from massive paired-end sequencing data
    • Korbel,J.O. et al. (2009) Pemer: a computational framework with simulation-based error models for inferring genomic structural variants from massive paired-end sequencing data. Genome Biol., 10, R23.
    • (2009) Genome Biol. , vol.10
    • Korbel, J.O.1
  • 27
    • 62349130698 scopus 로고    scopus 로고
    • Ultrafast and memory-efficient alignment of short dna sequences to the human genome
    • Langmead,B. et al. (2009) Ultrafast and memory-efficient alignment of short dna sequences to the human genome. Genome Biol., 10, R25.
    • (2009) Genome Biol. , vol.10
    • Langmead, B.1
  • 28
    • 67649580757 scopus 로고    scopus 로고
    • Modil: detecting small indels from clone-end sequencing with mixtures of distributions
    • Lee,S. et al. (2009) Modil: detecting small indels from clone-end sequencing with mixtures of distributions. Nat. Methods, 6, 473-474.
    • (2009) Nat. Methods , vol.6 , pp. 473-474
    • Lee, S.1
  • 29
    • 0036358995 scopus 로고    scopus 로고
    • The spectrum kernel: a string kernel for svm protein classification
    • Leslie,C. et al. (2002) The spectrum kernel: a string kernel for svm protein classification. In Proceedings of Pacific Symposium on Biocomputing, pp. 564-575.
    • (2002) Proceedings of Pacific Symposium on Biocomputing , pp. 564-575
    • Leslie, C.1
  • 30
    • 67649884743 scopus 로고    scopus 로고
    • Fast and accurate short read alignment with burrows-wheeler transform
    • Li,H. and Durbin,R. (2009) Fast and accurate short read alignment with burrows-wheeler transform. Bioinformatics, 25, 1754-1760.
    • (2009) Bioinformatics , vol.25 , pp. 1754-1760
    • Li, H.1    Durbin, R.2
  • 31
    • 77957272611 scopus 로고    scopus 로고
    • A survey of sequence alignment algorithms for nextgeneration sequencing
    • Li,H. and Homer,N. (2010) A survey of sequence alignment algorithms for nextgeneration sequencing. Brief. Bioinformatics, 11, 473-483.
    • (2010) Brief. Bioinformatics , vol.11 , pp. 473-483
    • Li, H.1    Homer, N.2
  • 32
    • 67650711615 scopus 로고    scopus 로고
    • Soap2: an improved ultrafast tool for short read alignment
    • Li,R. et al. (2009) Soap2: an improved ultrafast tool for short read alignment. Bioinformatics, 25, 1966-1967.
    • (2009) Bioinformatics , vol.25 , pp. 1966-1967
    • Li, R.1
  • 33
    • 79959929795 scopus 로고    scopus 로고
    • New powerful statistics for alignment-free sequence comparison under a pattern transfer model
    • Liu,X. et al. (2011) New powerful statistics for alignment-free sequence comparison under a pattern transfer model. J. Theo. Biol., 284, 106-116.
    • (2011) J. Theo. Biol. , vol.284 , pp. 106-116
    • Liu, X.1
  • 34
    • 79956307251 scopus 로고    scopus 로고
    • Stampy: A statistical algorithm for sensitive and fast mapping of illumina sequence reads
    • Lunter,G. and Goodson,M. (2011) Stampy: A statistical algorithm for sensitive and fast mapping of illumina sequence reads. Genome Res., 21, 936-939.
    • (2011) Genome Res. , vol.21 , pp. 936-939
    • Lunter, G.1    Goodson, M.2
  • 35
    • 77951962587 scopus 로고    scopus 로고
    • High quality SNP calling using Illumina data at shallow coverage
    • Malhis,N. and Jones, S.J.M. (2010) High quality SNP calling using Illumina data at shallow coverage. Bioinformatics (Oxford, England), 26, 1029-35.
    • (2010) Bioinformatics (Oxford, England) , vol.26 , pp. 1029-35
    • Malhis, N.1    Jones, S.J.M.2
  • 36
    • 33746203645 scopus 로고    scopus 로고
    • Ann: A library for approximate nearest neighbor searching
    • Available at, Accessed on July 18, 2012.
    • Mount,D.M. and Arya,S. (2010) Ann: A library for approximate nearest neighbor searching.Available at http://www.cs.umd.edu/ mount/ANN/.Accessed on July 18, 2012.
    • (2010)
    • Mount, D.M.1    Arya, S.2
  • 37
    • 70349675925 scopus 로고    scopus 로고
    • Fast approximate nearest neighbors with automatic algorithm configuration
    • Ranchordas, A. et al. (eds), INSTICC Press, Setubal, Portugal
    • Muja,M. and Lowe,D.G. (2009) Fast approximate nearest neighbors with automatic algorithm configuration. In Ranchordas, A. et al. (eds). International Conference on Computer Vision Theory and Application (VISSAPP'09), INSTICC Press, Setubal, Portugal, pp. 331-340.
    • (2009) International Conference on Computer Vision Theory and Application (VISSAPP'09) , pp. 331-340
    • Muja, M.1    Lowe, D.G.2
  • 38
    • 0000541351 scopus 로고    scopus 로고
    • A fast bit-vector algorithm for approximate string matching based on dynamic programming
    • Myers,G. (1999) A fast bit-vector algorithm for approximate string matching based on dynamic programming. J. ACM, 46, 395-415.
    • (1999) J. ACM , vol.46 , pp. 395-415
    • Myers, G.1
  • 39
    • 0345566149 scopus 로고    scopus 로고
    • A guided tour to approximate string matching
    • Navarro,G. (2001) A guided tour to approximate string matching. ACM Comput. Surv., 33, 31-88.
    • (2001) ACM Comput. Surv , vol.33 , pp. 31-88
    • Navarro, G.1
  • 40
    • 32644438405 scopus 로고    scopus 로고
    • Ametric index for approximate string matching
    • Navarro,G. and Chávez,E. (2006)Ametric index for approximate string matching. Theo. Comput. Sci., 352, 266-279.
    • (2006) Theo. Comput. Sci. , vol.352 , pp. 266-279
    • Navarro, G.1    Chávez, E.2
  • 41
    • 18544379601 scopus 로고    scopus 로고
    • Indexing text with approximate q-grams
    • Navarro,G. et al. (2005). Indexing text with approximate q-grams. J. Discrete Algorithms, 3, 157-175.
    • (2005) J. Discrete Algorithms , vol.3 , pp. 157-175
    • Navarro, G.1
  • 42
    • 0034764307 scopus 로고    scopus 로고
    • Ssaha:Afast search method for large dna databases
    • Ning,Z. et al. (2001) Ssaha:Afast search method for large dna databases. Genome Res., 11, 1725-1729.
    • (2001) Genome Res. , vol.11 , pp. 1725-1729
    • Ning, Z.1
  • 43
    • 40749155764 scopus 로고    scopus 로고
    • Effective indexing and filtering for similarity search in large biosequence databases
    • Washington, DC
    • Ozturk,O. and Ferhatosmanoglu,H. (2003) Effective indexing and filtering for similarity search in large biosequence databases. In BIBE, IEEE Computer Society, Washington, DC, pp. 359-366.
    • (2003) BIBE, IEEE Computer Society , pp. 359-366
    • Ozturk, O.1    Ferhatosmanoglu, H.2
  • 44
    • 33746253635 scopus 로고    scopus 로고
    • Vector space indexing for biosequence similarity searches
    • Ozturk,O. and Ferhatosmanoglu,H. (2005) Vector space indexing for biosequence similarity searches. Int. J. Artificial Intel. Tool, 14, 811-826.
    • (2005) Int. J. Artificial Intel. Tool , vol.14 , pp. 811-826
    • Ozturk, O.1    Ferhatosmanoglu, H.2
  • 45
    • 77953324416 scopus 로고    scopus 로고
    • Locality sensitive hashing: a comparison of hash function types and querying mechanisms
    • Paulevé,L. et al. (2010). Locality sensitive hashing: a comparison of hash function types and querying mechanisms. Pattern Reco. Lett., 31, 1348-1358.
    • (2010) Pattern Reco. Lett. , vol.31 , pp. 1348-1358
    • Paulevé, L.1
  • 46
    • 75149164526 scopus 로고    scopus 로고
    • Alignment-free sequence comparison (i): statistics and power
    • Reinert,G. et al. (2009) Alignment-free sequence comparison (i): statistics and power. J. Comput. Biol., 16, 1615-1634.
    • (2009) J. Comput. Biol. , vol.16 , pp. 1615-1634
    • Reinert, G.1
  • 47
    • 0000561280 scopus 로고
    • The r+-tree: A dynamic index for multi-dimensional objects
    • VLDB '87, Morgan Kaufmann Publishers Inc, San Francisco
    • Sellis,T.K. et al. (1987) The r+-tree: A dynamic index for multi-dimensional objects. In: Proceedings of the 13th International Conference on Very Large Data Bases, VLDB '87, Morgan Kaufmann Publishers Inc, San Francisco, pp. 507-518.
    • (1987) Proceedings of the 13th International Conference on Very Large Data Bases , pp. 507-518
    • Sellis, T.K.1
  • 48
    • 77952620021 scopus 로고    scopus 로고
    • On the collapse of q-Gram filtration
    • Carleton University, Ottawa, ON, Canada
    • Sutinen,E. and Szpankowski,W. (1998) On the collapse of q-Gram filtration. In FUN with Algorithms, Carleton University, Ottawa, ON, Canada, pp. 178-193.
    • (1998) FUN with Algorithms , pp. 178-193
    • Sutinen, E.1    Szpankowski, W.2
  • 49
    • 67349084049 scopus 로고    scopus 로고
    • Estimation of bacterial species phylogeny through oligonucleotide frequency distances
    • Takahashi,M. et al. (2009) Estimation of bacterial species phylogeny through oligonucleotide frequency distances. Genomics, 93, 525-533.
    • (2009) Genomics , vol.93 , pp. 525-533
    • Takahashi, M.1
  • 50
    • 84975742565 scopus 로고    scopus 로고
    • Amap of human genome variation from population-scale sequencing
    • The 1000 Genomes Project Consortium
    • The 1000 Genomes Project Consortium (2010) Amap of human genome variation from population-scale sequencing. Nature, 467, 1061-1073.
    • (2010) Nature , vol.467 , pp. 1061-1073
  • 51
    • 79959524146 scopus 로고    scopus 로고
    • A haplotype map of the human genome
    • The International HapMap Consortium
    • The International HapMap Consortium (2005) A haplotype map of the human genome. Nature, 437, 1299-1320.
    • (2005) Nature , vol.437 , pp. 1299-1320
  • 52
    • 0027113212 scopus 로고
    • Approximate string matching with q-grams and maximal matches
    • Ukkonen,E. (1992) Approximate string matching with q-grams and maximal matches. Theor. Comput. Sci., 92, 191-211.
    • (1992) Theor. Comput. Sci. , vol.92 , pp. 191-211
    • Ukkonen, E.1
  • 54
    • 34250391491 scopus 로고
    • Design and implementation of an efficient priority queue
    • van Emde Boas,P. et al. (1976) Design and implementation of an efficient priority queue. Theo. Comput. Syst., 10, 99-127.
    • (1976) Theo. Comput. Syst. , vol.10 , pp. 99-127
    • van Emde Boas, P.1
  • 55
    • 78349292948 scopus 로고    scopus 로고
    • Alignment-free sequence comparison (ii): theoretical power of comparison statistics
    • Wan,L. et al. (2010) Alignment-free sequence comparison (ii): theoretical power of comparison statistics. J. Comput. Biol., 17, 1467-1490.
    • (2010) J. Comput. Biol. , vol.17 , pp. 1467-1490
    • Wan, L.1
  • 56
    • 69749106334 scopus 로고    scopus 로고
    • Razers fast read mapping with sensitivity control
    • Weese,D. et al. (2009) Razers fast read mapping with sensitivity control. Genome Res., 19, 1646-1654.
    • (2009) Genome Res. , vol.19 , pp. 1646-1654
    • Weese, D.1
  • 57
    • 77952757244 scopus 로고    scopus 로고
    • Approximate string search in spatial databases
    • Li, F. et al. (eds), IEEE Computer Society, Washington, DC
    • Yao,B. et al. (2010) Approximate string search in spatial databases. In Li, F. et al. (eds). ICDE, IEEE Computer Society, Washington, DC, pp. 545-556.
    • (2010) ICDE , pp. 545-556
    • Yao, B.1


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