메뉴 건너뛰기




Volumn 19, Issue 10, 2012, Pages 1162-1175

SLIQ: Simple linear inequalities for efficient contig scaffolding

Author keywords

algorithms; biochemical networks; combinatorics; computational molecular biology; evolution; gene expressions; gene networks; genetic variation; graph theory; graphs and networks; next generation sequencing

Indexed keywords

ALGORITHM; ARTICLE; CONTIG MAPPING; DNA SEQUENCE; HUMAN; HUMAN GENOME; METHODOLOGY;

EID: 84867500400     PISSN: 10665277     EISSN: None     Source Type: Journal    
DOI: 10.1089/cmb.2011.0263     Document Type: Article
Times cited : (7)

References (19)
  • 1
    • 0036144823 scopus 로고    scopus 로고
    • Arachne: A whole-genome shotgun assembler
    • Batzoglou, S., Jaffe, D.B., Stanley, K., et al. 2002. Arachne: a whole-genome shotgun assembler. Genome Res 12, 177-189.
    • (2002) Genome Res , vol.12 , pp. 177-189
    • Batzoglou, S.1    Jaffe, D.B.2    Stanley, K.3
  • 2
    • 79951530130 scopus 로고    scopus 로고
    • Scaffolding pre-assembled contigs using SSPACE
    • Boetzer, M., Henkel, C.V., Jansen, H.J., et al. 2011. Scaffolding pre-assembled contigs using SSPACE. Bioinformatics 27, 578-579.
    • (2011) Bioinformatics , vol.27 , pp. 578-579
    • Boetzer, M.1    Henkel, C.V.2    Jansen, H.J.3
  • 3
    • 43149086380 scopus 로고    scopus 로고
    • Allpaths: De novo assembly of whole-genome shotgun microreads
    • Butler, J., MacCallum, I., Kleber, M., et al. 2008. Allpaths: de novo assembly of whole-genome shotgun microreads. Genome Res. 18, 810-820.
    • (2008) Genome Res. , vol.18 , pp. 810-820
    • Butler, J.1    MacCallum, I.2    Kleber, M.3
  • 4
    • 80051839847 scopus 로고    scopus 로고
    • Meraculous: De novo genome assembly with short paired-end reads
    • Chapman, J.A., Ho, I., Sunkara, S., et al. 2011. Meraculous: de novo genome assembly with short paired-end reads. PLoS One 6, e23501.
    • (2011) PLoS One , vol.6
    • Chapman, J.A.1    Ho, I.2    Sunkara, S.3
  • 5
    • 77954324418 scopus 로고    scopus 로고
    • Sopra: Scaffolding algorithm for paired reads via statistical optimization
    • Dayarian, A., Michael, T.P., and Sengupta, A.M. 2010. Sopra: Scaffolding algorithm for paired reads via statistical optimization. BMC Bioinformatics 11, 345.
    • (2010) BMC Bioinformatics , vol.11 , pp. 345
    • Dayarian, A.1    Michael, T.P.2    Sengupta, A.M.3
  • 6
    • 58149291658 scopus 로고    scopus 로고
    • De novo assembly of the pseudomonas syringae pv. syringae b728a genome using Illumina/Solexa short sequence reads
    • Farrer, R.A., Kemen, E., Jones, J.D.G., et al. 2009. De novo assembly of the pseudomonas syringae pv. syringae b728a genome using Illumina/Solexa short sequence reads. FEMS Microbiol Lett. 291, 103-111.
    • (2009) FEMS Microbiol Lett. , vol.291 , pp. 103-111
    • Farrer, R.A.1    Kemen, E.2    Jones, J.D.G.3
  • 7
    • 79953216356 scopus 로고    scopus 로고
    • Opera: Reconstructing optimal genomic scaffolds with high-throughput paired-end sequences
    • Gao, S., Nagarajan, N., and kin Sung, W. 2011. Opera: Reconstructing optimal genomic scaffolds with high-throughput paired-end sequences. LNBI. 6577, 437-451.
    • (2011) LNBI , vol.6577 , pp. 437-451
    • Gao, S.1    Nagarajan, N.2    Kin Sung, W.3
  • 9
    • 79952178131 scopus 로고    scopus 로고
    • High-quality draft assemblies of mammalian genomes from massively parallel sequence data
    • Gnerre, S., Maccallum, I., Przybylski, D., et al. 2011. High-quality draft assemblies of mammalian genomes from massively parallel sequence data. Proc Natl Acad Sci U S A. 108, 1513-1518.
    • (2011) Proc Natl Acad Sci U S A. , vol.108 , pp. 1513-1518
    • Gnerre, S.1    MacCallum, I.2    Przybylski, D.3
  • 10
  • 11
    • 84976669902 scopus 로고
    • Efficient algorithms for graph manipulation
    • Hopcroft, J., and Tarjan, R. 1973. Efficient algorithms for graph manipulation. Communications of the ACM. 16, 372-378.
    • (1973) Communications of the ACM. , vol.16 , pp. 372-378
    • Hopcroft, J.1    Tarjan, R.2
  • 12
    • 1242281253 scopus 로고    scopus 로고
    • The greedy path-merging algorithm for contig scaffolding
    • Huson, D.H., Reinert, K., and Myers, E. 2002. The greedy path-merging algorithm for contig scaffolding. Journal of the ACM. 49, 603-615.
    • (2002) Journal of the ACM , vol.49 , pp. 603-615
    • Huson, D.H.1    Reinert, K.2    Myers, E.3
  • 13
    • 0001909598 scopus 로고
    • Finding all the elementary circuits of a directed graph
    • Johnson, D.B. 1975. Finding all the elementary circuits of a directed graph. SIAM Journal on Computing. 4, 77-84.
    • (1975) SIAM Journal on Computing , vol.4 , pp. 77-84
    • Johnson, D.B.1
  • 14
    • 80054896129 scopus 로고    scopus 로고
    • Bambus 2: Scaffolding metagenomes
    • Koren, S., Treangen, T.J., and Pop, M. 2011. Bambus 2: scaffolding metagenomes. Bioinformatics. 27, 2964-2971.
    • (2011) Bioinformatics , vol.27 , pp. 2964-2971
    • Koren, S.1    Treangen, T.J.2    Pop, M.3
  • 15
    • 62349130698 scopus 로고    scopus 로고
    • Ultrafast and memory-efficient alignment of short dna sequences to the human genome
    • Langmead, B., Trapnell, C., Pop, M., 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    Trapnell, C.2    Pop, M.3
  • 16
    • 75649124547 scopus 로고    scopus 로고
    • De novo assembly of human genomes with massively parallel short read sequencing
    • Li, R., Zhu, H., Ruan, J., et al. 2010. De novo assembly of human genomes with massively parallel short read sequencing. Genome Res. 20, 265-272.
    • (2010) Genome Res. , vol.20 , pp. 265-272
    • Li, R.1    Zhu, H.2    Ruan, J.3
  • 17
    • 0346505466 scopus 로고    scopus 로고
    • Hierarchical scaffolding with Bambus
    • Pop, M., Kosack, D.S., and Salzberg, S.L. 2004. Hierarchical scaffolding with Bambus. Genome Res. 14, 149-159.
    • (2004) Genome Res. , vol.14 , pp. 149-159
    • Pop, M.1    Kosack, D.S.2    Salzberg, S.L.3
  • 18
    • 82255185486 scopus 로고    scopus 로고
    • Fast scaffolding with small independent mixed integer programs
    • Salmela, L., Mkinen, V., Vlimki, N., et al. 2011. Fast scaffolding with small independent mixed integer programs. Bioinformatics 27, 3259-3265
    • (2011) Bioinformatics , vol.27 , pp. 3259-3265
    • Salmela, L.1    Mkinen, V.2    Vlimki, N.3
  • 19
    • 43149115851 scopus 로고    scopus 로고
    • Velvet: Algorithms for de novo short read assembly using de Bruijn graphs
    • Zerbino, D.R., and Birney, E. 2008. Velvet: algorithms for de novo short read assembly using de Bruijn graphs. Genome Res. 18, 821-829.
    • (2008) Genome Res. , vol.18 , pp. 821-829
    • Zerbino, D.R.1    Birney, E.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.