publication . Article . Other literature type . 2010

progressiveMauve: Multiple Genome Alignment with Gene Gain, Loss and Rearrangement

Bob Mau; Aaron E. Darling; Nicole T. Perna;
Open Access English
  • Published: 01 Jun 2010 Journal: PLoS ONE, volume 5, issue 6 (eissn: 1932-6203, Copyright policy)
  • Publisher: Public Library of Science
Abstract
Background Multiple genome alignment remains a challenging problem. Effects of recombination including rearrangement, segmental duplication, gain, and loss can create a mosaic pattern of homology even among closely related organisms. Methodology/Principal Findings We describe a new method to align two or more genomes that have undergone rearrangements due to recombination and substantial amounts of segmental gain and loss (flux). We demonstrate that the new method can accurately align regions conserved in some, but not all, of the genomes, an important case not handled by our previous work. The method uses a novel alignment objective score called a sum-of-pairs ...
Subjects
free text keywords: Research Article, Computational Biology/Comparative Sequence Analysis, Computational Biology/Genomics, Genetics and Genomics/Comparative Genomics, Genetics and Genomics/Microbial Evolution and Genomics, Medicine, R, Science, Q, Genomics, Segmental duplication, Population, education.field_of_study, education, Gene rearrangement, Sequence alignment, Computational biology, Genetics, Biology, Genome, Comparative genomics, Genome evolution
Funded by
NIH| Molecular Evolution of Microbial Pathogen Genomes
Project
  • Funder: National Institutes of Health (NIH)
  • Project Code: 5R01GM062994-05
  • Funding stream: NATIONAL INSTITUTE OF GENERAL MEDICAL SCIENCES
,
NSF| Postdoctoral Research Fellowship in Biological Informatics FY 2006
Project
  • Funder: National Science Foundation (NSF)
  • Project Code: 0630765
  • Funding stream: Directorate for Biological Sciences | Division of Biological Infrastructure
75 references, page 1 of 5

Kumar, S, Filipski, A. Multiple sequence alignment: In pursuit of homologous DNA positions.. Genome Res. 2007; 17: 127-135 [OpenAIRE] [PubMed]

Lunter, G. Probabilistic whole-genome alignments reveal high indel rates in the human and mouse genomes.. Bioinformatics. 2007; 23 [OpenAIRE]

Prakash, A, Tompa, M. Measuring the accuracy of genome-size multiple alignments.. Genome Biology. 2007; 8: R124+ [OpenAIRE] [PubMed]

Dewey, CN, Pachter, L. Evolution at the nucleotide level: the problem of multiple whole-genome alignment.. Hum Mol Genet. 2006; 15 (Suppl 1) [OpenAIRE]

Fitch, WM. Homology: a personal view on some of the problems.. Trends Genet. 2000; 16: 227-231 [PubMed]

Delcher, AL, Kasif, S, Fleischmann, RD, Peterson, J, White, O. Alignment of whole genomes.. Nucleic Acids Res. 1999; 27: 2369-76 [OpenAIRE] [PubMed]

Delcher, AL, Phillippy, A, Carlton, J, Salzberg, SL. Fast algorithms for large-scale genome alignment and comparison.. Nucleic acids research. 2002; 30: 2478-2483 [OpenAIRE] [PubMed]

Kurtz, S, Phillippy, A, Delcher, AL, Smoot, M, Shumway, M. Versatile and open software for comparing large genomes.. Genome Biol. 2004; 5: R12 [OpenAIRE] [PubMed]

Darling, ACE, Mau, B, Blattner, FR, Perna, NT. Mauve: multiple alignment of conserved genomic sequence with rearrangements.. Genome Res. 2004; 14: 1394-403 [OpenAIRE] [PubMed]

Perna, NT, Plunkett, G, Burland, V, Mau, B, Glasner, JD. Genome sequence of enterohaemorrhagic Escherichia coli O157:H7.. Nature. 2001; 409: 529-33 [PubMed]

Welch, RA, Burland, V, Plunkett, G, Redford, P, Roesch, P. Extensive mosaic structure revealed by the complete genome sequence of uropathogenic Escherichia coli.. Proc Natl Acad Sci U S A. 2002; 99: 17020-4 [OpenAIRE] [PubMed]

Hogg, JS, Hu, FZ, Janto, B, Boissy, R, Hayes, J. Characterization and modeling of the Haemophilus influenzae core- and supra-genomes based on the complete genomic sequences of Rd and 12 clinical nontypeable strains.. Genome Biology. 2007; 8: R103+ [OpenAIRE] [PubMed]

Hsiao, WW, Ung, K, Aeschliman, D, Bryan, J, Finlay, BB. Evidence of a large novel gene pool associated with prokaryotic genomic islands.. PLoS Genetics. 2005; 1: e62+ [OpenAIRE] [PubMed]

Tettelin, H, Masignani, V, Cieslewicz, MJ, Donati, C, Medini, D. Genome analysis of multiple pathogenic isolates of Streptococcus agalactiae: implications for the microbial “pan-genome”.. Proc Natl Acad Sci U S A. 2005; 102: 13950-13955 [OpenAIRE] [PubMed]

Vernikos, GS, Thomson, NR, Parkhill, J. Genetic flux over time in the Salmonella lineage.. Genome Biology. 2007; 8: R100+ [OpenAIRE] [PubMed]

75 references, page 1 of 5
Abstract
Background Multiple genome alignment remains a challenging problem. Effects of recombination including rearrangement, segmental duplication, gain, and loss can create a mosaic pattern of homology even among closely related organisms. Methodology/Principal Findings We describe a new method to align two or more genomes that have undergone rearrangements due to recombination and substantial amounts of segmental gain and loss (flux). We demonstrate that the new method can accurately align regions conserved in some, but not all, of the genomes, an important case not handled by our previous work. The method uses a novel alignment objective score called a sum-of-pairs ...
Subjects
free text keywords: Research Article, Computational Biology/Comparative Sequence Analysis, Computational Biology/Genomics, Genetics and Genomics/Comparative Genomics, Genetics and Genomics/Microbial Evolution and Genomics, Medicine, R, Science, Q, Genomics, Segmental duplication, Population, education.field_of_study, education, Gene rearrangement, Sequence alignment, Computational biology, Genetics, Biology, Genome, Comparative genomics, Genome evolution
Funded by
NIH| Molecular Evolution of Microbial Pathogen Genomes
Project
  • Funder: National Institutes of Health (NIH)
  • Project Code: 5R01GM062994-05
  • Funding stream: NATIONAL INSTITUTE OF GENERAL MEDICAL SCIENCES
,
NSF| Postdoctoral Research Fellowship in Biological Informatics FY 2006
Project
  • Funder: National Science Foundation (NSF)
  • Project Code: 0630765
  • Funding stream: Directorate for Biological Sciences | Division of Biological Infrastructure
75 references, page 1 of 5

Kumar, S, Filipski, A. Multiple sequence alignment: In pursuit of homologous DNA positions.. Genome Res. 2007; 17: 127-135 [OpenAIRE] [PubMed]

Lunter, G. Probabilistic whole-genome alignments reveal high indel rates in the human and mouse genomes.. Bioinformatics. 2007; 23 [OpenAIRE]

Prakash, A, Tompa, M. Measuring the accuracy of genome-size multiple alignments.. Genome Biology. 2007; 8: R124+ [OpenAIRE] [PubMed]

Dewey, CN, Pachter, L. Evolution at the nucleotide level: the problem of multiple whole-genome alignment.. Hum Mol Genet. 2006; 15 (Suppl 1) [OpenAIRE]

Fitch, WM. Homology: a personal view on some of the problems.. Trends Genet. 2000; 16: 227-231 [PubMed]

Delcher, AL, Kasif, S, Fleischmann, RD, Peterson, J, White, O. Alignment of whole genomes.. Nucleic Acids Res. 1999; 27: 2369-76 [OpenAIRE] [PubMed]

Delcher, AL, Phillippy, A, Carlton, J, Salzberg, SL. Fast algorithms for large-scale genome alignment and comparison.. Nucleic acids research. 2002; 30: 2478-2483 [OpenAIRE] [PubMed]

Kurtz, S, Phillippy, A, Delcher, AL, Smoot, M, Shumway, M. Versatile and open software for comparing large genomes.. Genome Biol. 2004; 5: R12 [OpenAIRE] [PubMed]

Darling, ACE, Mau, B, Blattner, FR, Perna, NT. Mauve: multiple alignment of conserved genomic sequence with rearrangements.. Genome Res. 2004; 14: 1394-403 [OpenAIRE] [PubMed]

Perna, NT, Plunkett, G, Burland, V, Mau, B, Glasner, JD. Genome sequence of enterohaemorrhagic Escherichia coli O157:H7.. Nature. 2001; 409: 529-33 [PubMed]

Welch, RA, Burland, V, Plunkett, G, Redford, P, Roesch, P. Extensive mosaic structure revealed by the complete genome sequence of uropathogenic Escherichia coli.. Proc Natl Acad Sci U S A. 2002; 99: 17020-4 [OpenAIRE] [PubMed]

Hogg, JS, Hu, FZ, Janto, B, Boissy, R, Hayes, J. Characterization and modeling of the Haemophilus influenzae core- and supra-genomes based on the complete genomic sequences of Rd and 12 clinical nontypeable strains.. Genome Biology. 2007; 8: R103+ [OpenAIRE] [PubMed]

Hsiao, WW, Ung, K, Aeschliman, D, Bryan, J, Finlay, BB. Evidence of a large novel gene pool associated with prokaryotic genomic islands.. PLoS Genetics. 2005; 1: e62+ [OpenAIRE] [PubMed]

Tettelin, H, Masignani, V, Cieslewicz, MJ, Donati, C, Medini, D. Genome analysis of multiple pathogenic isolates of Streptococcus agalactiae: implications for the microbial “pan-genome”.. Proc Natl Acad Sci U S A. 2005; 102: 13950-13955 [OpenAIRE] [PubMed]

Vernikos, GS, Thomson, NR, Parkhill, J. Genetic flux over time in the Salmonella lineage.. Genome Biology. 2007; 8: R100+ [OpenAIRE] [PubMed]

75 references, page 1 of 5
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