Skip to main content
SpringerLink
Log in
Book cover

Evolutionary Genomics pp 237–257Cite as

Whole-Genome Alignment

  • Protocol
  • First Online:

Part of the book series: Methods in Molecular Biology ((MIMB,volume 855))

Abstract

Whole-genome alignment (WGA) is the prediction of evolutionary relationships at the nucleotide level between two or more genomes. It combines aspects of both colinear sequence alignment and gene orthology prediction, and is typically more challenging to address than either of these tasks due to the size and complexity of whole genomes. Despite the difficulty of this problem, numerous methods have been developed for its solution because WGAs are valuable for genome-wide analyses, such as phylogenetic inference, genome annotation, and function prediction. In this chapter, we discuss the meaning and significance of WGA and present an overview of the methods that address it. We also examine the problem of evaluating whole-genome aligners and offer a set of methodological challenges that need to be tackled in order to make the most effective use of our rapidly growing databases of whole genomes.

This is a preview of subscription content, log in via an institution.

Protocol
USD   49.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD   89.00
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD   119.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD   169.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Learn about institutional subscriptions

Springer Nature is developing a new tool to find and evaluate Protocols. Learn more

References

  1. 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

    Google Scholar 

  2. Fleischmann RD, Adams MD, White O, et al. (1995) Whole-genome random sequencing and assembly of Haemophilus influenzae Rd. Science 269:496–512

    Article  PubMed  CAS  Google Scholar 

  3. Kyrpides NC (1999) Genomes OnLine Database (GOLD 1.0): a monitor of complete and ongoing genome projects world-wide. Bioinformatics 15:773–4

    Article  PubMed  CAS  Google Scholar 

  4. Fitch WM (1970) Distinguishing homologous from analogous proteins. Systematic Zoology 19:99–113

    Article  PubMed  CAS  Google Scholar 

  5. 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

    Google Scholar 

  6. Dewey CN (2011) Positional orthology: putting genomic evolutionary relationships into context. Briefings in Bioinformatics. doi:10.1093/bib/bbr040

  7. Dewey CN, Pachter L (2006) Evolution at the nucleotide level: the problem of multiple whole-genome alignment. Human Molecular Genetics 15:R51–R56

    Article  PubMed  CAS  Google Scholar 

  8. Blanchette M, Kent WJ, Riemer C, et al. (2004) Aligning multiple genomic sequences with the threaded blockset aligner. Genome Research 14:708–15

    Article  PubMed  CAS  Google Scholar 

  9. Ma J, Ratan A, Raney BJ, et al. (2008) The infinite sites model of genome evolution. Proceedings of the National Academy of Sciences of the United States of America 105:14254–61

    Article  PubMed  CAS  Google Scholar 

  10. 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

    Article  PubMed  CAS  Google Scholar 

  11. Smith TF, Waterman MS (1981) Identification of common molecular subsequences. Journal of Molecular Biology 147:195–7

    Article  PubMed  CAS  Google Scholar 

  12. Tesler G (2002) GRIMM: genome rearrangements web server. Bioinformatics 18:492–3

    Article  PubMed  CAS  Google Scholar 

  13. Paten B, Herrero J, Fitzgerald S, et al. (2008) Genome-wide nucleotide-level mammalian ancestor reconstruction. Genome Research 18:1829–43

    Article  PubMed  CAS  Google Scholar 

  14. Ma J, Zhang L, Suh BB, et al. (2006) Reconstructing contiguous regions of an ancestral genome. Genome Research 16:1557–65

    Article  PubMed  CAS  Google Scholar 

  15. Stark A, Lin MF, Kheradpour P, et al. (2007) Discovery of functional elements in 12 Drosophila genomes using evolutionary signatures. Nature 450:219–232

    Article  PubMed  CAS  Google Scholar 

  16. 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

    Google Scholar 

  17. Eddy SR (2002) Computational genomics of noncoding RNA genes. Cell 109:137–40

    Article  PubMed  CAS  Google Scholar 

  18. Margulies EH, Blanchette M, Haussler D, et al. (2003) Identification and characterization of multi-species conserved sequences. Genome Research 13:2507–18

    Article  PubMed  CAS  Google Scholar 

  19. 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

    Article  PubMed  CAS  Google Scholar 

  20. Bejerano G, Pheasant M, Makunin I, et al. (2004) Ultraconserved elements in the human genome. Science 304:1321–5

    Article  PubMed  CAS  Google Scholar 

  21. Altschul SF, Gish W, Miller W, et al. (1990) Basic local alignment search tool. Journal of Molecular Biology 215:403–10

    PubMed  CAS  Google Scholar 

  22. Altschul SF, Madden TL, Schäffer AA, et al. (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Research 25:3389–402

    Article  PubMed  CAS  Google Scholar 

  23. Brudno M, Malde S, Poliakov A, et al. (2003) Glocal alignment: finding rearrangements during alignment. Bioinformatics 19 Suppl 1:i54–62

    Article  PubMed  Google Scholar 

  24. Ma B, Tromp J, Li M (2002) PatternHunter: faster and more sensitive homology search. Bioinformatics 18:440–5

    Article  PubMed  CAS  Google Scholar 

  25. Sun Y, Buhler J (2004) Designing multiple simultaneous seeds for DNA similarity search. In: Proceedings of the eighth annual international conference on Resaerch in computational molecular biology, 76–84. ACM

    Google Scholar 

  26. Xu J, Brown D, Li M, et al. (2006) Optimizing multiple spaced seeds for homology search. Journal of Computational Biology 13:1355–68

    Article  PubMed  CAS  Google Scholar 

  27. Zhang L (2007) Superiority of spaced seeds for homology search. IEEE/ACM Transactions on Computational Biology and Bioinformatics 4:496–505

    Article  PubMed  CAS  Google Scholar 

  28. Schwartz S, Kent WJ, Smit A, et al. (2003) Human-mouse alignments with BLASTZ. Genome Research 13:103–7

    Article  PubMed  CAS  Google Scholar 

  29. Delcher AL, Kasif S, Fleischmann RD, et al. (1999) Alignment of whole genomes. Nucleic Acids Research 27:2369–76

    Article  PubMed  CAS  Google Scholar 

  30. Brudno M, Chapman M, Göttgens B, et al. (2003) Fast and sensitive multiple alignment of large genomic sequences. BMC Bioinformatics 4:66

    Article  PubMed  Google Scholar 

  31. Brudno M, Do CB, Cooper GM, et al. (2003) LAGAN and Multi-LAGAN: efficient tools for large-scale multiple alignment of genomic DNA. Genome Research 13:721–31

    Article  PubMed  CAS  Google Scholar 

  32. Gusfield D (1997) Algorithms on strings, trees, and sequences: computer science and computational biology. Cambridge University Press, Cambridge

    Book  Google Scholar 

  33. Pevzner P, Tesler G (2003) Genome rearrangements in mammalian evolution: lessons from human and mouse genomes. Genome Research 13:37–45

    Article  PubMed  CAS  Google Scholar 

  34. Pham SK, Pevzner PA (2010) DRIMM-Synteny: decomposing genomes into evolutionary conserved segments. Bioinformatics 26:2509–16

    Article  PubMed  CAS  Google Scholar 

  35. Dewey CN (2007) Aligning multiple whole genomes with Mercator and MAVID. In: Bergman N (ed) Methods in Molecular Biology, volume 395, 221–36. Humana Press, Clifton, NJ

    Google Scholar 

  36. 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

    Article  PubMed  CAS  Google Scholar 

  37. Hachiya T, Osana Y, Popendorf K, et al. (2009) Accurate identification of orthologous segments among multiple genomes. Bioinformatics 25:853–60

    Article  PubMed  CAS  Google Scholar 

  38. Dubchak I, Poliakov A, Kislyuk A, et al. (2009) Multiple whole-genome alignments without a reference organism. Genome Research 19:682–9

    Article  PubMed  CAS  Google Scholar 

  39. Darling AE, Mau B, Perna NT (2010) progressiveMauve: Multiple Genome Alignment with Gene Gain, Loss and Rearrangement. PLoS One 5:e11147

    Article  Google Scholar 

  40. Angiuoli SV, Salzberg SL (2010) Mugsy: Fast multiple alignment of closely related whole genomes. Bioinformatics 27:334–342

    Article  PubMed  Google Scholar 

  41. Pevzner PA, Pevzner PA, Tang H, et al. (2004) De novo repeat classification and fragment assembly. Genome Research 14:1786–96

    Article  PubMed  CAS  Google Scholar 

  42. Paten B, Diekhans M, Earl D, et al. (2011) Cactus graphs for genome comparisons. Journal of Computational Biology 18:469–81

    Article  PubMed  CAS  Google Scholar 

  43. Bray N, Pachter L (2004) MAVID: constrained ancestral alignment of multiple sequences. Genome Research 14:693–9

    Article  PubMed  CAS  Google Scholar 

  44. Rausch T, Emde AK, Weese D, et al. (2008) Segment-based multiple sequence alignment. Bioinformatics 24:i187–92

    Article  PubMed  Google Scholar 

  45. Bradley RK, Roberts A, Smoot M, et al. (2009) Fast statistical alignment. PLoS Computational Biology 5:e1000392

    Article  Google Scholar 

  46. Slater GSC, Birney E (2005) Automated generation of heuristics for biological sequence comparison. BMC Bioinformatics 6:31

    Article  PubMed  Google Scholar 

  47. Flicek P, Amode MR, Barrell D, et al. (2011) Ensembl 2011. Nucleic Acids Research 39:D800–6

    Article  PubMed  Google Scholar 

  48. Frazer KA, Pachter L, Poliakov A, et al. (2004) VISTA: computational tools for comparative genomics. Nucleic Acids Research 32:W273–9

    Article  PubMed  CAS  Google Scholar 

  49. Kent WJ, Sugnet CW, Furey TS, et al. (2002) The Human Genome Browser at UCSC. Genome Research 12:996–1006

    PubMed  CAS  Google Scholar 

  50. Kent WJ, Baertsch R, Hinrichs A, et al. (2003) Evolution’s cauldron: duplication, deletion, and rearrangement in the mouse and human genomes. Proceedings of the National Academy of Sciences of the United States of America 100:11484–9

    Article  PubMed  CAS  Google Scholar 

  51. Darling ACE, Mau B, Blattner FR, et al. (2004) Mauve: multiple alignment of conserved genomic sequence with rearrangements. Genome Research 14:1394–403

    Article  PubMed  CAS  Google Scholar 

  52. Edgar RC, Asimenos G, Batzoglou S, et al. Evolver: a whole-genome sequence evolution simulator http://www.drive5.com/evolver. Accessed 11 July 2011

  53. Stoye J, Evers D, Meyer F (1998) Rose: generating sequence families. Bioinformatics 14:157–63

    Article  PubMed  CAS  Google Scholar 

  54. Cartwright RA (2005) DNA assembly with gaps (Dawg): simulating sequence evolution. Bioinformatics 21:iii31–8

    Article  PubMed  CAS  Google Scholar 

  55. 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

    Article  PubMed  Google Scholar 

  56. Varadarajan A, Bradley RK, Holmes IH (2008) Tools for simulating evolution of aligned genomic regions with integrated parameter estimation. Genome Biology 9:R147

    Article  PubMed  Google Scholar 

  57. Fletcher W, Yang Z (2009) INDELible: a flexible simulator of biological sequence evolution. Molecular Biology and Evolution 26:1879–88

    Article  PubMed  CAS  Google Scholar 

  58. Kim J, Sinha S (2010) Towards realistic benchmarks for multiple alignments of non-coding sequences. BMC Bioinformatics 11:54

    Article  PubMed  Google Scholar 

  59. Margulies EH, Cooper GM, Asimenos G, et al. (2007) Analyses of deep mammalian sequence alignments and constraint predictions for 1% of the human genome. Genome Research 17:760–774

    Article  PubMed  CAS  Google Scholar 

  60. Morgenstern B, Rinner O, Abdeddaïm S, et al. (2002) Exon discovery by genomic sequence alignment. Bioinformatics 18:777–87

    Article  PubMed  CAS  Google Scholar 

  61. Genome 10K Community of Scientists (2009) Genome 10K: a proposal to obtain whole-genome sequence for 10,000 vertebrate species. The Journal of Heredity 100:659–74

    Article  Google Scholar 

  62. Lunter G, Rocco A, Mimouni N, et al. (2008) Uncertainty in homology inferences: Assessing and improving genomic sequence alignment. Genome Research 18:298–309

    Article  PubMed  CAS  Google Scholar 

Download references

Author information

Authors and Affiliations

  1. Biostatistics and Medical Informatics and Computer Sciences, Genome Center of Wisconsin, University of Wisconsin-Madison, Madison, WI, USA

    Colin N. Dewey

Authors
  1. Colin N. Dewey
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Colin N. Dewey .

Editor information

Editors and Affiliations

  1. Department of Computer Science, ETH Zürich, Universitätsstr. 6, Zürich, 8092, Switzerland

    Maria Anisimova

Rights and permissions

Reprints and permissions

Copyright information

© 2012 Springer Science+Business Media, LLC

About this protocol

Cite this protocol

Dewey, C.N. (2012). Whole-Genome Alignment. In: Anisimova, M. (eds) Evolutionary Genomics. Methods in Molecular Biology, vol 855. Humana Press, Totowa, NJ. https://doi.org/10.1007/978-1-61779-582-4_8

Download citation

  • DOI: https://doi.org/10.1007/978-1-61779-582-4_8

  • Published:

  • Publisher Name: Humana Press, Totowa, NJ

  • Print ISBN: 978-1-61779-581-7

  • Online ISBN: 978-1-61779-582-4

  • eBook Packages: Springer Protocols

Publish with us

Policies and ethics

Search

Navigation