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Volumn 29, Issue 23, 2013, Pages 2987-2994

FPSAC: Fast phylogenetic scaffolding of ancient contigs

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIAL GENOME; CLASSIFICATION; COMPUTER PROGRAM; COMPUTER SIMULATION; CONTIG MAPPING; DNA SEQUENCE; GENETICS; MICROBIOLOGY; MOLECULAR EVOLUTION; PHYLOGENY; PLAGUE; PROCEDURES; YERSINIA PESTIS; ARTICLE; METHODOLOGY;

EID: 84890088964     PISSN: 13674803     EISSN: 14602059     Source Type: Journal    
DOI: 10.1093/bioinformatics/btt527     Document Type: Article
Times cited : (25)

References (61)
  • 1
    • 66049158304 scopus 로고    scopus 로고
    • Breakpoint graphs and ancestral genome reconstructions
    • Alekseyev, M.A. and Pevzner, P.A. (2009) Breakpoint graphs and ancestral genome reconstructions. Genome Res., 19, 943-957.
    • (2009) Genome Res. , vol.19 , pp. 943-957
    • Alekseyev, M.A.1    Pevzner, P.A.2
  • 2
    • 79551599525 scopus 로고    scopus 로고
    • Mugsy: Fast multiple alignment of closely related whole genomes
    • Angiuoli, S.V. and Salzberg, S.L. (2011) Mugsy: fast multiple alignment of closely related whole genomes. Bioinformatics, 27, 334-342.
    • (2011) Bioinformatics , vol.27 , pp. 334-342
    • Angiuoli, S.V.1    Salzberg, S.L.2
  • 3
    • 84863664355 scopus 로고    scopus 로고
    • A hybrid approach for the automated finishing of bacterial genomes
    • Bashir, A. et al. (2012) A hybrid approach for the automated finishing of bacterial genomes. Nat. Biotechnol., 30, 701-707.
    • (2012) Nat. Biotechnol. , vol.30 , pp. 701-707
    • Bashir, A.1
  • 4
    • 84866448711 scopus 로고    scopus 로고
    • Evolution of gene neighborhoods within reconciled phylogenies
    • Be'rard, S. et al. (2012) Evolution of gene neighborhoods within reconciled phylogenies. Bioinformatics, 28, i382-i388.
    • (2012) Bioinformatics , vol.28
    • Be'Rard, S.1
  • 5
    • 78049476016 scopus 로고    scopus 로고
    • Reconstruction of ancestral genome subject to whole genome duplication, speciation, rearrangement and loss
    • Singh, M. and Moulton, V. (eds) Liverpool, UK, September 6-8, 2010. Proceedings 6293 of Lecture Notes in Bioinformatics. Springer Verlag.
    • Bertrand, D. et al. (2010) Reconstruction of ancestral genome subject to whole genome duplication, speciation, rearrangement and loss. In: Singh, M. and Moulton, V. (eds) Algorithms in Bioinformatics, 10th International Workshop, WABI 2010, Liverpool, UK, September 6-8, 2010. Proceedings, volume 6293 of Lecture Notes in Bioinformatics. pages 78-89. Springer Verlag.
    • (2010) Algorithms in Bioinformatics, 10th International Workshop, WABI 2010 , pp. 78-89
    • Bertrand, D.1
  • 6
    • 10944228197 scopus 로고    scopus 로고
    • Reconstructing large regions of an ancestral mammalian genome in silico
    • Blanchette, M. et al. (2004) Reconstructing large regions of an ancestral mammalian genome in silico. Genome Res., 14, 2412-2423.
    • (2004) Genome Res. , vol.14 , pp. 2412-2423
    • Blanchette, M.1
  • 7
    • 80054987989 scopus 로고    scopus 로고
    • A draft genome of Yersinia pestis from victims of the Black Death
    • Bos, K.I. et al. (2011) A draft genome of Yersinia pestis from victims of the Black Death. Nature, 478, 506-510.
    • (2011) Nature , vol.478 , pp. 506-510
    • Bos, K.I.1
  • 8
    • 4644293305 scopus 로고    scopus 로고
    • Insights into the evolution of Yersinia pestis through wholegenome comparison with yersinia pseudotuberculosis
    • Chain, P. et al. (2004) Insights into the evolution of Yersinia pestis through wholegenome comparison with yersinia pseudotuberculosis. Proc. Natl Acad. Sci. USA, 101, 13826-13831.
    • (2004) Proc. Natl Acad. Sci. USA , vol.101 , pp. 13826-13831
    • Chain, P.1
  • 9
    • 80051839847 scopus 로고    scopus 로고
    • Meraculous: De novo genome assembly with short pairedend reads
    • Chapman, J. et al. (2011) Meraculous: De novo genome assembly with short pairedend reads. PLoS One, 6, e23501.
    • (2011) PLoS One , vol.6
    • Chapman, J.1
  • 10
    • 57149085266 scopus 로고    scopus 로고
    • A methodological framework for the reconstruction of contiguous regions of ancestral genomes and its application to mammalian genomes
    • Chauve, C. and Tannier, E. (2008) A methodological framework for the reconstruction of contiguous regions of ancestral genomes and its application to mammalian genomes. PLoS Comput. Biol., 4, e1000234.
    • (2008) PLoS Comput. Biol. , vol.4
    • Chauve, C.1    Tannier, E.2
  • 11
    • 77958065555 scopus 로고    scopus 로고
    • Yeast ancestral genome reconstructions: The possibilities of computational methods II
    • Chauve, C. et al. (2010) Yeast ancestral genome reconstructions: the possibilities of computational methods II. J. Comput. Biol., 17, 1097-1112.
    • (2010) J. Comput. Biol. , vol.17 , pp. 1097-1112
    • Chauve, C.1
  • 12
    • 84890069974 scopus 로고    scopus 로고
    • Hypergraph covering problems motivated by genome assembly questions (short abstract). to appear in the proceedings of
    • Chauve, C. et al. (2013) Hypergraph covering problems motivated by genome assembly questions (short abstract). To appear in the proceedings of. International Workshop On Combinatorial Algorithms, 2013.
    • (2013) International Workshop on Combinatorial Algorithms , pp. 2013
    • Chauve, C.1
  • 13
    • 78149254832 scopus 로고    scopus 로고
    • Gloome: Gain loss mapping engine
    • Cohen, O. et al. (2010) Gloome: gain loss mapping engine. Bioinformatics, 26, 2914-2915.
    • (2010) Bioinformatics , vol.26 , pp. 2914-2915
    • Cohen, O.1
  • 14
    • 77955038643 scopus 로고    scopus 로고
    • Count evolutionary analysis of phylogenetic profiles with parsimony and likelihood
    • Csurös, M. (2010) Count: evolutionary analysis of phylogenetic profiles with parsimony and likelihood. Bioinformatics, 26, 1910-1912.
    • (2010) Bioinformatics , vol.26 , pp. 1910-1912
    • Csurös, M.1
  • 15
    • 48249144818 scopus 로고    scopus 로고
    • Dynamics of genome rearrangement in bacterial populations
    • Darling, A.E. et al. (2008) Dynamics of genome rearrangement in bacterial populations. PLoS Genet., 4, e1000128.
    • (2008) PLoS Genet. , vol.4
    • Darling, A.E.1
  • 16
    • 0036330894 scopus 로고    scopus 로고
    • Genome sequence of Yersinia pestis KIM
    • Deng, W. et al. (2002) Genome sequence of Yersinia pestis KIM. J. Bacteriol., 184, 4601-4611.
    • (2002) J. Bacteriol. , vol.184 , pp. 4601-4611
    • Deng, W.1
  • 17
    • 75249091585 scopus 로고    scopus 로고
    • Ancestors 1.0: A web server for ancestral sequence reconstruction
    • Diallo, A.B. et al. (2010) Ancestors 1.0: a web server for ancestral sequence reconstruction. Bioinformatics, 26, 130-131.
    • (2010) Bioinformatics , vol.26 , pp. 130-131
    • Diallo, A.B.1
  • 18
    • 79960700334 scopus 로고    scopus 로고
    • Palaegenomics of Mycobacterium tuberculosis: Epidemic burst with a degrading genome
    • Djelouadji, Z. et al. (2011) Palaegenomics of Mycobacterium tuberculosis: epidemic burst with a degrading genome. Lancet Infect. Dis., 11, 641-650.
    • (2011) Lancet Infect. Dis. , vol.11 , pp. 641-650
    • Djelouadji, Z.1
  • 19
    • 84874330144 scopus 로고    scopus 로고
    • Scarpa: Scaffolding reads with practical algorithms
    • Donmez, N. and Brudno, M. (2013) Scarpa: scaffolding reads with practical algorithms. Bioinformatics, 29, 428-434.
    • (2013) Bioinformatics , vol.29 , pp. 428-434
    • Donmez, N.1    Brudno, M.2
  • 20
    • 79959306149 scopus 로고    scopus 로고
    • Insights gained from paleomicrobiology into ancient and modern tuberculosis
    • Donoghue, H. (2011) Insights gained from paleomicrobiology into ancient and modern tuberculosis. Clin. Microbiol. Infect., 17, 821-829.
    • (2011) Clin. Microbiol. Infect. , vol.17 , pp. 821-829
    • Donoghue, H.1
  • 21
    • 33646455056 scopus 로고    scopus 로고
    • Pathogenic microbial ancient DNA: A problem or an opportunity
    • Donoghue, H. and Spigelman, M. (2006) Pathogenic microbial ancient DNA: a problem or an opportunity. Proc. R. Soc. B, 273, 641-642.
    • (2006) Proc. R. Soc. B , vol.273 , pp. 641-642
    • Donoghue, H.1    Spigelman, M.2
  • 22
    • 84857569500 scopus 로고    scopus 로고
    • Plague in the genomic area
    • Drancourt, M. (2012) Plague in the genomic area. Clin. Microbiol. Infect., 18, 224-230.
    • (2012) Clin. Microbiol. Infect. , vol.18 , pp. 224-230
    • Drancourt, M.1
  • 23
    • 11144345147 scopus 로고    scopus 로고
    • Palaemicrobiology: Current issues and perspectives
    • Drancourt, M. and Raoult, D. (2005) Palaemicrobiology: current issues and perspectives. Nat. Rev. Microbiol., 3, 23-35.
    • (2005) Nat. Rev. Microbiol. , vol.3 , pp. 23-35
    • Drancourt, M.1    Raoult, D.2
  • 24
    • 3042666256 scopus 로고    scopus 로고
    • Muscle: Multiple sequence alignment with high accuracy and high throughput
    • Edgar, R.C. (2004) Muscle: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res., 32, 1792-1797.
    • (2004) Nucleic Acids Res. , vol.32 , pp. 1792-1797
    • Edgar, R.C.1
  • 25
    • 84959747425 scopus 로고
    • Toward defining the course of evolution: Minimum change for a specified tree topology
    • Fitch, W.M. (1971) Toward defining the course of evolution: minimum change for a specified tree topology. Syst. Zool., 20, 406-416.
    • (1971) Syst. Zool. , vol.20 , pp. 406-416
    • Fitch, W.M.1
  • 26
    • 34249854264 scopus 로고    scopus 로고
    • Phylogenetic exploration of bacterial genomic rearrangements
    • Fremez, R. et al. (2007) Phylogenetic exploration of bacterial genomic rearrangements. Bioinformatics, 23, 1172-1174.
    • (2007) Bioinformatics , vol.23 , pp. 1172-1174
    • Fremez, R.1
  • 27
    • 80955159932 scopus 로고    scopus 로고
    • Opera: Reconstructing optimal genomic scaffolds with highthroughput paired-end sequences
    • Gao, S. et al. (2011) Opera: reconstructing optimal genomic scaffolds with highthroughput paired-end sequences. J. Comput. Biol., 18, 1681-1691.
    • (2011) J. Comput. Biol. , vol.18 , pp. 1681-1691
    • Gao, S.1
  • 28
    • 70350012234 scopus 로고    scopus 로고
    • Assisted assembly: How to improve a de novo genome assembly by using related species
    • Gnerre, S. et al. (2009) Assisted assembly: how to improve a de novo genome assembly by using related species. Genome Biol., 10, R88.
    • (2009) Genome Biol. , vol.10
    • Gnerre, S.1
  • 29
    • 67149106149 scopus 로고    scopus 로고
    • Additions, losses, and rearrangements on the evolutionary route from a reconstructed ancestor to the modern saccharomyces cerevisiae genome
    • Gordon, J.L. et al. (2009) Additions, losses, and rearrangements on the evolutionary route from a reconstructed ancestor to the modern saccharomyces cerevisiae genome. PLoS Genet., 5, e1000485.
    • (2009) PLoS Genet. , vol.5
    • Gordon, J.L.1
  • 31
    • 84866465344 scopus 로고    scopus 로고
    • ANGES: Reconstructing ancestral genomes maps
    • Jones, B.R. et al. (2012) ANGES: Reconstructing ancestral genomes maps. Bioinformatics, 28, 2388-2390.
    • (2012) Bioinformatics , vol.28 , pp. 2388-2390
    • Jones, B.R.1
  • 32
    • 84873175933 scopus 로고    scopus 로고
    • Reference-assisted chromosome assembly
    • Kim, J. et al. (2013) Reference-assisted chromosome assembly. Proc. Natl Acad. Sci. USA, 110, 1785-1790.
    • (2013) Proc. Natl Acad. Sci. USA , vol.110 , pp. 1785-1790
    • Kim, J.1
  • 33
    • 69649109364 scopus 로고    scopus 로고
    • Circos: An information aesthetic for comparative genomics
    • Krzywinski, M. et al. (2009) Circos: an information aesthetic for comparative genomics. Genome Res., 19, 1639-1645.
    • (2009) Genome Res. , vol.19 , pp. 1639-1645
    • Krzywinski, M.1
  • 35
    • 84864476435 scopus 로고    scopus 로고
    • AGORA: Assembly guided by optical restriction alignment
    • Lin, H. et al. (2012) AGORA: Assembly guided by optical restriction alignment. BMC Bioinformatics, 13, 189.
    • (2012) BMC Bioinformatics , vol.13 , pp. 189
    • Lin, H.1
  • 36
    • 33750386912 scopus 로고    scopus 로고
    • Reconstructing contiguous regions of an ancestral genome
    • Ma, J. et al. (2006) Reconstructing contiguous regions of an ancestral genome. Genome Res., 16, 1557-1565.
    • (2006) Genome Res. , vol.16 , pp. 1557-1565
    • Ma, J.1
  • 37
    • 52449090559 scopus 로고    scopus 로고
    • Dupcar: Reconstructing contiguous ancestral regions with duplications
    • Ma, J. et al. (2008) Dupcar: reconstructing contiguous ancestral regions with duplications. J. Comput. Biol., 15, 1007-1027.
    • (2008) J. Comput. Biol. , vol.15 , pp. 1007-1027
    • Ma, J.1
  • 38
    • 84878073917 scopus 로고    scopus 로고
    • Linearization of ancestral multichromosomal genomes
    • Manuch, J. et al. (2012) Linearization of ancestral multichromosomal genomes. BMC Bioinformatics, 13(Suppl. 19), S11.
    • (2012) BMC Bioinformatics , vol.13 , Issue.SUPPL. 19
    • Manuch, J.1
  • 39
    • 79951749932 scopus 로고    scopus 로고
    • Bayesian sampling of genomic rearrangement scenarios via double cut and join
    • Miklós, I. and Tannier, E. (2010) Bayesian sampling of genomic rearrangement scenarios via double cut and join. Bioinformatics, 26, 3012-3019.
    • (2010) Bioinformatics , vol.26 , pp. 3012-3019
    • Miklós, I.1    Tannier, E.2
  • 40
    • 84890107116 scopus 로고    scopus 로고
    • Minkin, I. et al. (2013) Sibelia. http://bioinf.spbau.ru/sibelia.
    • (2013) Sibelia
    • Minkin, I.1
  • 41
    • 77951972053 scopus 로고    scopus 로고
    • Genomicus: A database and a browser to study gene synteny in modern and ancestral genomes
    • Muffato, M. et al. (2010) Genomicus: a database and a browser to study gene synteny in modern and ancestral genomes. Bioinformatics, 26, 1119-1121.
    • (2010) Bioinformatics , vol.26 , pp. 1119-1121
    • Muffato, M.1
  • 42
    • 77953019477 scopus 로고    scopus 로고
    • Scaffold filling, contig fusion and comparative gene order inference
    • Munoz, A. et al. (2010) Scaffold filling, contig fusion and comparative gene order inference. BMC Bioinformatics, 11, 304.
    • (2010) BMC Bioinformatics , vol.11 , pp. 304
    • Munoz, A.1
  • 43
    • 78649312312 scopus 로고    scopus 로고
    • Ancestral grass karyotype reconstruction unravels new mechanisms of genome shuffling as a source of plant evolution
    • Murat, F. et al. (2010) Ancestral grass karyotype reconstruction unravels new mechanisms of genome shuffling as a source of plant evolution. Genome Res., 20, 1545-1557.
    • (2010) Genome Res. , vol.20 , pp. 1545-1557
    • Murat, F.1
  • 44
    • 80053442046 scopus 로고    scopus 로고
    • Reconstructing the architecture of the ancestral amniote genome
    • Ouangraoua, A. et al. (2011) Reconstructing the architecture of the ancestral amniote genome. Bioinformatics, 27, 2664-2671.
    • (2011) Bioinformatics , vol.27 , pp. 2664-2671
    • Ouangraoua, A.1
  • 45
    • 80054924581 scopus 로고    scopus 로고
    • Bacterial epidemiology and biology - Lessons from genome sequencing
    • Parkhill, J. and Wren, B.W. (2011) Bacterial epidemiology and biology - lessons from genome sequencing. Genome Biol., 12, 230.
    • (2011) Genome Biol. , vol.12 , pp. 230
    • Parkhill, J.1    Wren, B.W.2
  • 46
    • 84865176493 scopus 로고    scopus 로고
    • Scaling metagenome sequence assembly with probabilistic de bruijn graphs
    • Pell, J. et al. (2012) Scaling metagenome sequence assembly with probabilistic de bruijn graphs. Proc. Natl Acad. Sci. USA, 109, 13272-13277.
    • (2012) Proc. Natl Acad. Sci. USA , vol.109 , pp. 13272-13277
    • Pell, J.1
  • 47
    • 34447300950 scopus 로고    scopus 로고
    • Sea anemone genome reveals ancestral eumetazoan gene repertoire and genomic organization
    • Putnam, N.H. et al. (2007) Sea anemone genome reveals ancestral eumetazoan gene repertoire and genomic organization. Science, 317, 86-94.
    • (2007) Science , vol.317 , pp. 86-94
    • Putnam, N.H.1
  • 48
    • 84868327508 scopus 로고    scopus 로고
    • Finished bacterial genomes from shotgun sequence data
    • Ribeiro, F.J. et al. (2012) Finished bacterial genomes from shotgun sequence data. Genome Res., 22, 2270-2277.
    • (2012) Genome Res. , vol.22 , pp. 2270-2277
    • Ribeiro, F.J.1
  • 49
    • 68549115571 scopus 로고    scopus 로고
    • Reordering contigs of draft genomes using the mauve aligner
    • Rissman, A.I. et al. (2009) Reordering contigs of draft genomes using the mauve aligner. Bioinformatics, 25, 2071-2073.
    • (2009) Bioinformatics , vol.25 , pp. 2071-2073
    • Rissman, A.I.1
  • 50
    • 84867500400 scopus 로고    scopus 로고
    • Sliq: Simple linear inequalities for efficient contig scaffolding
    • Roy, R.S. et al. (2012) Sliq: Simple linear inequalities for efficient contig scaffolding. J. Comput. Biol., 19, 1162-1175.
    • (2012) J. Comput. Biol. , vol.19 , pp. 1162-1175
    • Roy, R.S.1
  • 51
    • 82255185486 scopus 로고    scopus 로고
    • Fast scaffolding with small independent mixed integer programs
    • Salmela, L. 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
  • 52
    • 70349811330 scopus 로고    scopus 로고
    • Towards improved reconstruction of ancestral gene order in angiosperm phylogeny
    • Sankoff, D. et al. (2009) Towards improved reconstruction of ancestral gene order in angiosperm phylogeny. J. Comput. Biol., 16, 1353-1367.
    • (2009) J. Comput. Biol. , vol.16 , pp. 1353-1367
    • Sankoff, D.1
  • 53
    • 84860683374 scopus 로고    scopus 로고
    • Improving ancient DNA read mapping against modern reference genomes
    • Schubert, M. et al. (2012) Improving ancient DNA read mapping against modern reference genomes. BMC Genomics, 13, 178.
    • (2012) BMC Genomics , vol.13 , pp. 178
    • Schubert, M.1
  • 54
    • 80053137140 scopus 로고    scopus 로고
    • Targeted enrichment of ancient pathogens yielding the pPCP1 plasmid of Yersinia pestis from victims of the black death
    • Schuenemann, V.J. et al. (2011) Targeted enrichment of ancient pathogens yielding the pPCP1 plasmid of Yersinia pestis from victims of the black death. Proc. Natl Acad. Sci. USA, 108, E746-E752.
    • (2011) Proc. Natl Acad. Sci. USA , vol.108
    • Schuenemann, V.J.1
  • 55
    • 84867904826 scopus 로고    scopus 로고
    • Phylogenetic modeling of lateral gene transfer reconstructs the pattern and relative timing of speciations
    • Szöllosi, G.J. et al. (2012) Phylogenetic modeling of lateral gene transfer reconstructs the pattern and relative timing of speciations. Proc. Natl Acad. Sci. USA, 109, 17513-17518.
    • (2012) Proc. Natl Acad. Sci. USA , vol.109 , pp. 17513-17518
    • Szöllosi, G.J.1
  • 56
    • 83855165105 scopus 로고    scopus 로고
    • Repetitive DNA and next-generation sequencing: Computational challenges and solutions
    • Treangen, T.J. and Salzberg, S.L. (2012) Repetitive DNA and next-generation sequencing: computational challenges and solutions. Nat. Rev. Genet., 13, 36-46.
    • (2012) Nat. Rev. Genet. , vol.13 , pp. 36-46
    • Treangen, T.J.1    Salzberg, S.L.2
  • 57
    • 33645396934 scopus 로고    scopus 로고
    • Reconstruction of ancient genome and gene order from complete microbial genome sequences
    • Wang, Y. et al. (2006) Reconstruction of ancient genome and gene order from complete microbial genome sequences. J. Theoret. Biol., 239, 494-498.
    • (2006) J. Theoret. Biol. , vol.239 , pp. 494-498
    • Wang, Y.1
  • 58
    • 84866928158 scopus 로고    scopus 로고
    • Insights from genomics into bacterial pathogen populations
    • Wilson, D. (2012) Insights from genomics into bacterial pathogen populations. PLoS Pathog., 8, e1002874.
    • (2012) PLoS Pathog. , vol.8
    • Wilson, D.1
  • 59
    • 80052635569 scopus 로고    scopus 로고
    • Consistency of sequence-based gene clusters
    • Wittler, R. et al. (2011) Consistency of sequence-based gene clusters. J. Comput. Biol., 18, 1023-1039.
    • (2011) J. Comput. Biol. , vol.18 , pp. 1023-1039
    • Wittler, R.1
  • 60
    • 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
  • 61
    • 0034053725 scopus 로고    scopus 로고
    • A greedy algorithm for aligning DNA sequences
    • Zhang, Z. et al. (2000) A greedy algorithm for aligning DNA sequences. J. Comput. Biol., 7, 203-214.
    • (2000) J. Comput. Biol. , vol.7 , pp. 203-214
    • Zhang, Z.1


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