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Volumn 855, Issue , 2012, Pages 237-257

Whole-genome alignment

Author keywords

Comparative genomics; Genome evolution; Orthology map; Sequence alignment; Toporthology; Whole genome alignment

Indexed keywords

ANIMAL; ARTICLE; GENETIC DATABASE; GENETICS; GENOME; GENOMICS; HUMAN; METHODOLOGY; MOLECULAR EVOLUTION; SEQUENCE ALIGNMENT;

EID: 84860014577     PISSN: 10643745     EISSN: None     Source Type: Book Series    
DOI: 10.1007/978-1-61779-582-4_8     Document Type: Article
Times cited : (24)

References (62)
  • 1
    • 84859974402 scopus 로고    scopus 로고
    • Alignment methods strategies challenges benchmarking and comparative overview
    • In Anisimova, M. ed. Evolutionary genomics: Statistical and computational methods Springer Science+ Business media LLC
    • Loytynoja A (2012) Alignment methods strategies, challenges, benchmarking, and comparative overview. In Anisimova, M., (ed.), Evolutionary genomics: statistical and computational methods (volume 1). Methods in Molecular Biology, Springer Science+ Business media, LLC
    • (2012) Methods in Molecular Biology , vol.1
    • Loytynoja, A.1
  • 2
    • 0029653518 scopus 로고
    • Whole-genome random sequencing and assembly of haemophilus influenzae Rd
    • Fleischmann RD, Adams MD, White O, et al. (1995) Whole-genome random sequencing and assembly of Haemophilus influenzae Rd. Science 269:496-512
    • (1995) Science , vol.269 , pp. 496-512
    • Fleischmann, R.D.1    Adams, M.D.2    White, O.3
  • 3
    • 0032873141 scopus 로고    scopus 로고
    • Genomes Online Database (GOLD 1.0): A monitor of complete and ongoing genome projects world-wide
    • DOI 10.1093/bioinformatics/15.9.773
    • Kyrpides NC (1999) Genomes OnLine Database (GOLD 1.0): a monitor of complete and ongoing genome projects world-wide. Bioinformatics 15:773-4 (Pubitemid 29485394)
    • (1999) Bioinformatics , vol.15 , Issue.9 , pp. 773-774
    • Kyrpides, N.C.1
  • 4
    • 0014800108 scopus 로고
    • Distinguishing homologous from analogous proteins
    • Fitch WM (1970) Distinguishing homologous from analogous proteins. Systematic Zoology 19:99-113
    • (1970) Systematic Zoology , vol.19 , pp. 99-113
    • Fitch, W.M.1
  • 5
    • 84859995792 scopus 로고    scopus 로고
    • Inferring orthology and paralogy
    • In Anisimova M. ed Evolutionary genomics: Statistical and computational methods Springer Science+ Business media LLC
    • Altenhoff AM, Dessimoz C (2012) Inferring orthology and paralogy. In Anisimova, M., (ed.), Evolutionary genomics: statistical and computational methods (volume 1). Methods in Molecular Biology, Springer Science+ Business media, LLC
    • (2012) Methods in Molecular Biology , vol.1
    • Altenhoff, A.M.1    Dessimoz, C.2
  • 6
    • 80053195352 scopus 로고    scopus 로고
    • Positional orthology: Putting genomic evolutionary relationships into context
    • 10.1093 bib bbr040
    • Dewey CN (2011) Positional orthology: putting genomic evolutionary relationships into context. Briefings in Bioinformatics. doi:10.1093/bib/bbr040
    • (2011) Briefings in Bioinformatics
    • Dewey, C.N.1
  • 7
    • 33746400697 scopus 로고    scopus 로고
    • Evolution at the nucleotide level: The problem of multiple whole-genome alignment
    • Dewey CN, Pachter L (2006) Evolution at the nucleotide level: the problem of multiple whole-genome alignment. Human Molecular Genetics 15:R51-R56
    • (2006) Human Molecular Genetics , vol.15
    • Dewey, C.N.1    Pachter, L.2
  • 10
    • 0014757386 scopus 로고
    • A general method applicable to the search for similarities in the amino acid sequence of two proteins
    • Needleman SB, Wunsch CD (1970) A general method applicable to the search for similarities in the amino acid sequence of two proteins. Journal of Molecular Biology 48:443-53
    • (1970) Journal of Molecular Biology , vol.48 , pp. 443-453
    • Needleman, S.B.1    Wunsch, C.D.2
  • 12
    • 0036211065 scopus 로고    scopus 로고
    • GRIMM: Genome rearrangements web server
    • Tesler G (2002) GRIMM: genome rearrangements web server. Bioinformatics 18:492-3 (Pubitemid 34284955)
    • (2002) Bioinformatics , vol.18 , Issue.3 , pp. 492-493
    • Tesler, G.1
  • 13
    • 55549095155 scopus 로고    scopus 로고
    • Genome-wide nucleotide-level mammalian ancestor reconstruction
    • Paten B, Herrero J, Fitzgerald S, et al. (2008) Genome-wide nucleotide-level mammalian ancestor reconstruction. Genome Research 18:1829-43
    • (2008) Genome Research , vol.18 , pp. 1829-1843
    • Paten, B.1    Herrero, J.2    Fitzgerald, S.3
  • 16
    • 84859992627 scopus 로고    scopus 로고
    • Gene prediction
    • In Anisimova M. ed Evolutionary genomics: Statistical and computational methods Springer Science+Business media LLC
    • Alioto T (2012) Gene prediction. In Anisimova, M., (ed.), Evolutionary genomics: statistical and computational methods (volume 1). Methods in Molecular Biology, Springer Science+Business media, LLC
    • (2012) Methods in Molecular Biology , vol.1
    • Alioto, T.1
  • 17
    • 0037133945 scopus 로고    scopus 로고
    • Computational genomics of noncoding RNA genes
    • DOI 10.1016/S0092-8674(02)00727-4
    • Eddy SR (2002) Computational genomics of noncoding RNA genes. Cell 109:137-40 (Pubitemid 34518250)
    • (2002) Cell , vol.109 , Issue.2 , pp. 137-140
    • Eddy, S.R.1
  • 19
    • 0023821768 scopus 로고
    • Embryonic epsilon and gamma globin genes of a prosimian primate galago crassicaudatus nucleotide and amino acid sequences developmental regulation and phylogenetic footprints
    • Tagle DA, Koop BF, Goodman M, et al. (1988) Embryonic epsilon and gamma globin genes of a prosimian primate (Galago crassicaudatus). Nucleotide and amino acid sequences, developmental regulation and phylogenetic footprints. Journal of Molecular Biology 203:439-55
    • (1988) Journal of Molecular Biology , vol.203 , pp. 439-455
    • Tagle, D.A.1    Koop, B.F.2    Goodman, M.3
  • 24
    • 0036202921 scopus 로고    scopus 로고
    • PatternHunter: Faster and more sensitive homology search
    • Ma B, Tromp J, Li M (2002) PatternHunter: faster and more sensitive homology search. Bioinformatics 18:440-5 (Pubitemid 34284945)
    • (2002) Bioinformatics , vol.18 , Issue.3 , pp. 440-445
    • Ma, B.1    Tromp, J.2    Li, M.3
  • 26
    • 33846254599 scopus 로고    scopus 로고
    • Optimizing multiple spaced seeds for homology search
    • DOI 10.1089/cmb.2006.13.1355
    • Xu J, Brown D, Li M, et al. (2006) Optimizing multiple spaced seeds for homology search. Journal of Computational Biology 13:1355-68 (Pubitemid 46100698)
    • (2006) Journal of Computational Biology , vol.13 , Issue.7 , pp. 1355-1368
    • Xu, J.1    Brown, D.2    Li, M.3    Ma, B.4
  • 28
  • 30
    • 2942603015 scopus 로고    scopus 로고
    • Fast and sensitive multiple alignment of large genomic sequences
    • Brudno M, Chapman M, Göttgens B, et al. (2003) Fast and sensitive multiple alignment of large genomic sequences. BMC Bioinformatics 4:66
    • (2003) BMC Bioinformatics , vol.4 , pp. 66
    • Brudno, M.1    Chapman, M.2    Göttgens, B.3
  • 33
    • 0037264074 scopus 로고    scopus 로고
    • Genome rearrangements in mammalian evolution: Lessons from human and mouse genomes
    • Pevzner P, Tesler G (2003) Genome rearrangements in mammalian evolution: lessons from human and mouse genomes. Genome Research 13:37-45
    • (2003) Genome Research , vol.13 , pp. 37-45
    • Pevzner, P.1    Tesler, G.2
  • 34
    • 77957787194 scopus 로고    scopus 로고
    • Drimm-synteny: Decomposing genomes into evolutionary conserved segments
    • PhamSK, Pevzner PA (2010)DRIMM-Synteny: decomposing genomes into evolutionary conserved segments. Bioinformatics 26:2509-16
    • (2010) Bioinformatics , vol.26 , pp. 2509-2516
    • Pham, S.K.1    Pevzner, P.A.2
  • 35
    • 36549051577 scopus 로고    scopus 로고
    • Aligningmultiplewhole genomes with mercator and MAVID
    • Bergman N ed Humana Press Clifton NJ
    • DeweyCN(2007)Aligningmultiplewhole genomes with Mercator and MAVID. In: Bergman N (ed) Methods in Molecular Biology, volume 395, 221-36. Humana Press, Clifton, NJ
    • (2007) Methods in Molecular Biology , vol.395 , pp. 221-236
    • Dewey, C.N.1
  • 36
    • 54949108148 scopus 로고    scopus 로고
    • Enredo and pecan: Genome-wide mammalian consistency-based multiple alignment with paralogs
    • Paten B, Herrero J, Beal K, et al. (2008) Enredo and Pecan: genome-wide mammalian consistency-based multiple alignment with paralogs. Genome Research 18:1814-28
    • (2008) Genome Research , vol.18 , pp. 1814-1828
    • Paten, B.1    Herrero, J.2    Beal, K.3
  • 37
    • 63549088678 scopus 로고    scopus 로고
    • Accurate identification of orthologous segments among multiple genomes
    • Hachiya T, Osana Y, Popendorf K, et al. (2009) Accurate identification of orthologous segments among multiple genomes. Bioinformatics 25:853-60
    • (2009) Bioinformatics , vol.25 , pp. 853-860
    • Hachiya, T.1    Osana, Y.2    Popendorf, K.3
  • 38
    • 63849126687 scopus 로고    scopus 로고
    • Multiple whole-genome alignments without a reference organism
    • Dubchak I, Poliakov A, Kislyuk A, et al. (2009) Multiple whole-genome alignments without a reference organism. Genome Research 19:682-9
    • (2009) Genome Research , vol.19 , pp. 682-689
    • Dubchak, I.1    Poliakov, A.2    Kislyuk, A.3
  • 39
    • 77956193448 scopus 로고    scopus 로고
    • Progressive mauve: Multiple genome alignment with gene gain loss and rearrangement
    • Darling AE, Mau B, Perna NT (2010) progressiveMauve: Multiple Genome Alignment with Gene Gain, Loss and Rearrangement. PLoS One 5:e11147
    • (2010) PLoS One , vol.5
    • Darling, A.E.1    Mau, B.2    Perna, N.T.3
  • 40
    • 79551599525 scopus 로고    scopus 로고
    • Mugsy: Fast multiple alignment of closely related whole genomes
    • Angiuoli SV, Salzberg SL (2010) Mugsy: Fast multiple alignment of closely related whole genomes. Bioinformatics 27:334-342
    • (2010) Bioinformatics , vol.27 , pp. 334-342
    • Angiuoli, S.V.1    Salzberg, S.L.2
  • 41
    • 4644275238 scopus 로고    scopus 로고
    • De novo repeat classification and fragment assembly
    • DOI 10.1101/gr.2395204
    • Pevzner PA, Pevzner PA, Tang H, et al. (2004) De novo repeat classification and fragment assembly. Genome Research 14:1786-96 (Pubitemid 39276437)
    • (2004) Genome Research , vol.14 , Issue.9 , pp. 1786-1796
    • Pevzner, P.A.1    Tang, H.2    Tesler, G.3
  • 43
    • 1842667852 scopus 로고    scopus 로고
    • MAVID: Constrained ancestral alignment of multiple sequences
    • DOI 10.1101/gr.1960404
    • Bray N, Pachter L (2004) MAVID: constrained ancestral alignment of multiple sequences. Genome Research 14:693-9 (Pubitemid 38500242)
    • (2004) Genome Research , vol.14 , Issue.4 , pp. 693-699
    • Bray, N.1    Pachter, L.2
  • 44
    • 49549106252 scopus 로고    scopus 로고
    • Segment-based multiple sequence alignment
    • Rausch T, Emde AK, Weese D, et al. (2008) Segment-based multiple sequence alignment. Bioinformatics 24:i187-92
    • (2008) Bioinformatics , vol.24
    • Rausch, T.1    Emde, A.K.2    Weese, D.3
  • 46
    • 24044447664 scopus 로고    scopus 로고
    • Automated generation of heuristics for biological sequence comparison
    • Slater GSC, Birney E (2005) Automated generation of heuristics for biological sequence comparison. BMC Bioinformatics 6:31
    • (2005) BMC Bioinformatics , vol.6 , pp. 31
    • Slater, G.S.C.1    Birney, E.2
  • 51
    • 3543051830 scopus 로고    scopus 로고
    • Mauve: Multiple alignment of conserved genomic sequence with rearrangements
    • DOI 10.1101/gr.2289704
    • Darling ACE, Mau B, Blattner FR, et al. (2004) Mauve: multiple alignment of conserved genomic sequence with rearrangements. Genome Research 14:1394-403 (Pubitemid 39029237)
    • (2004) Genome Research , vol.14 , Issue.7 , pp. 1394-1403
    • Darling, A.C.E.1    Mau, B.2    Blattner, F.R.3    Perna, N.T.4
  • 53
    • 0031857684 scopus 로고    scopus 로고
    • Rose: Generating sequence families
    • Stoye J, Evers D, Meyer F (1998) Rose: generating sequence families. Bioinformatics 14:157-63 (Pubitemid 28395875)
    • (1998) Bioinformatics , vol.14 , Issue.2 , pp. 157-163
    • Stoye, J.1    Evers, D.2    Meyer, F.3
  • 54
    • 28944454501 scopus 로고    scopus 로고
    • DNA assembly with gaps (Dawg): Simulating sequence evolution
    • DOI 10.1093/bioinformatics/bti1200
    • Cartwright RA (2005) DNA assembly with gaps (Dawg): simulating sequence evolution. Bioinformatics 21:iii31-8 (Pubitemid 41782948)
    • (2005) Bioinformatics , vol.21 , Issue.SUPPL. 3
    • Cartwright, R.A.1
  • 55
    • 33750204634 scopus 로고    scopus 로고
    • Detecting the limits of regulatory element conservation and divergence estimation using pairwise and multiple alignments
    • Pollard DA, Moses AM, Iyer VN, et al. (2006) Detecting the limits of regulatory element conservation and divergence estimation using pairwise and multiple alignments. BMC Bioinformatics 7:376
    • (2006) BMC Bioinformatics , vol.7 , pp. 376
    • Pollard, D.A.1    Moses, A.M.2    Iyer, V.N.3
  • 56
    • 54949104412 scopus 로고    scopus 로고
    • Tools for simulating evolution of aligned genomic regions with integrated parameter estimation
    • Varadarajan A, Bradley RK,Holmes IH(2008) Tools for simulating evolution of aligned genomic regions with integrated parameter estimation. Genome Biology 9:R147
    • (2008) Genome Biology , vol.9
    • Varadarajan, A.1    Bradley, R.K.2    Holmes, I.H.3
  • 57
    • 67749108209 scopus 로고    scopus 로고
    • Indelible: A flexible simulator of biological sequence evolution
    • Fletcher W, Yang Z (2009) INDELible: a flexible simulator of biological sequence evolution. Molecular Biology and Evolution 26:1879-88
    • (2009) Molecular Biology and Evolution , vol.26 , pp. 1879-1888
    • Fletcher, W.1    Yang, Z.2
  • 58
    • 76949098763 scopus 로고    scopus 로고
    • Towards realisticbenchmarks for multiple alignments of noncodingsequences
    • Kim J, Sinha S (2010) Towards realisticbenchmarks for multiple alignments of noncodingsequences. BMC Bioinformatics 11:54
    • (2010) BMC Bioinformatics , vol.11 , pp. 54
    • Kim, J.1    Sinha, S.2
  • 61
    • 71049176982 scopus 로고    scopus 로고
    • Genome 10K: A proposal to obtain wholegenome sequence for 10 000 vertebrate species
    • Genome 10K Community of Scientists
    • Genome 10K Community of Scientists (2009) Genome 10K: a proposal to obtain wholegenome sequence for 10,000 vertebrate species. The Journal of Heredity 100:659-74
    • (2009) Journal of Heredity , vol.100 , pp. 659-674
  • 62
    • 39049145326 scopus 로고    scopus 로고
    • Uncertainty in homology inferences: Assessing and improving genomic sequence alignment
    • DOI 10.1101/gr.6725608
    • Lunter G, Rocco A, Mimouni N, et al. (2008) Uncertainty in homology inferences: Assessing and improving genomic sequence alignment. Genome Research 18:298-309(Pubitemid 351240740)
    • (2008) Genome Research , vol.18 , Issue.2 , pp. 298-309
    • Lunter, G.1    Rocco, A.2    Mimouni, N.3    Heger, A.4    Caldeira, A.5    Hein, J.6


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