Multiple Alignment of DNA Sequences with MAFFT (original) (raw)

References

1. Woese, C. R., and Fox, G. E. (1977) Phylogenetic structure of the prokaryotic domain: the primary kingdoms. Proc Natl Acad Sci USA 74, 5088–90.
   Article PubMed CAS Google Scholar
2. Flicek, P., Keibler, E., Hu, P., Korf, I., and Brent, M. R. (2003) Leveraging the mouse genome for gene prediction in human: from whole-genome shotgun reads to a global synteny map. Genome Res 13, 46–54.
   Article PubMed CAS Google Scholar
3. Katoh, K., Misawa, K., Kuma, K., and Miyata, T. (2002) MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform. Nucleic Acids Res 30, 3059–66.
   Article PubMed CAS Google Scholar
4. Katoh, K., Kuma, K., Toh, H., and Miyata, T. (2005) MAFFT version 5: improvement in accuracy of multiple sequence alignment. Nucleic Acids Res 33, 511–8.
   Article PubMed CAS Google Scholar
5. Wilm, A., Mainz, I., and Steger, G. (2006) An enhanced RNA alignment benchmark for sequence alignment programs. Algorithms Mol Biol 1, 19.
   Article PubMed Google Scholar
6. Carroll, H., Beckstead, W., O’connor, T., Ebbert, M., Clement, M., Snell, Q., and McClellan, D. (2007) DNA reference alignment benchmarks based on tertiary structure of encoded proteins. Bioinformatics 23, 2648–49.
   Google Scholar
7. Blanchette, M., Kent, W. J., Riemer, C., Elnitski, L., Smit, A. F., Roskin, K. M., Baertsch, R., Rosenbloom, K., Clawson, H., Green, E. D., Haussler, D., and Miller, W. (2004) Aligning multiple genomic sequences with the threaded blockset aligner. Genome Res 14, 708–15.
   Article PubMed CAS Google Scholar
8. http://www.bx.psu.edu/miller_lab
9. Darling, A. C., Mau, B., Blattner, F. R., and Perna, N. T. (2004) Mauve: multiple alignment of conserved genomic sequence with rearrangements. Genome Res 14, 1394–403.
   Article PubMed CAS Google Scholar
10. http://gel.ahabs.wisc.edu/mauve/
11. Edgar, R. C., and Batzoglou, S. (2006) Multiple sequence alignment. Curr Opin Struct Biol 16, 368–73.
    Article PubMed CAS Google Scholar
12. Needleman, S. B., and Wunsch, C. D. (1970) A general method applicable to the search for similarities in the amino acid sequence of two proteins. J Mol Biol 48, 443–53.
    Article PubMed CAS Google Scholar
13. Smith, T. F., and Waterman, M. S. (1981) Identification of common molecular subsequences. J Mol Biol 147, 195–7.
    Article PubMed CAS Google Scholar
14. Gotoh, O. (1982) An improved algorithm for matching biological sequences. J Mol Biol 162, 705–8.
    Article PubMed CAS Google Scholar
15. Feng, D. F., and Doolittle, R. F. (1987) Progressive sequence alignment as a prerequisite to correct phylogenetic trees. J Mol Evol 25, 351–60.
    Article PubMed CAS Google Scholar
16. Thompson, J. D., Higgins, D. G., and Gibson, T. J. (1994) CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res 22, 4673–80.
    Article PubMed CAS Google Scholar
17. Katoh, K., and Toh, H. (2007) Parttree: an algorithm to build an approximate tree from a large number of unaligned sequences. Bioinformatics 23, 372–4.
    Article PubMed CAS Google Scholar
18. Barton, G. J., and Sternberg, M. J. (1987) A strategy for the rapid multiple alignment of protein sequences. confidence levels from tertiary structure comparisons. J Mol Biol 198, 327–37.
    Article PubMed CAS Google Scholar
19. Berger, M. P., and Munson, P. J. (1991) A novel randomized iterative strategy for aligning multiple protein sequences. Comput Appl Biosci 7, 479–84.
    PubMed CAS Google Scholar
20. Gotoh, O. (1993) Optimal alignment between groups of sequences and its application to multiple sequence alignment. Comput Appl Biosci 9, 361–70.
    PubMed CAS Google Scholar
21. Ishikawa, M., Toya, T., Hoshida, M., Nitta, K., Ogiwara, A., and Kanehisa, M. (1993) Multiple sequence alignment by parallel simulated annealing. Comput Appl Biosci 9, 267–73.
    PubMed CAS Google Scholar
22. Notredame, C., and Higgins, D. G. (1996) Saga: sequence alignment by genetic algorithm. Nucleic Acids Res 24, 1515–24.
    Article PubMed CAS Google Scholar
23. Gotoh, O. (1994) Further improvement in methods of group-to-group sequence alignment with generalized profile operations. Comput Appl Biosci 10, 379–87.
    PubMed CAS Google Scholar
24. Gotoh, O. (1995) A weighting system and algorithm for aligning many phylogenetically related sequences. Comput Appl Biosci 11, 543–51.
    PubMed CAS Google Scholar
25. Gotoh, O. (1996) Significant improvement in accuracy of multiple protein sequence alignments by iterative refinement as assessed by reference to structural alignments. J Mol Biol 264, 823–38.
    Article PubMed CAS Google Scholar
26. Hirosawa, M., Totoki, Y., Hoshida, M., and Ishikawa, M. (1995) Comprehensive study on iterative algorithms of multiple sequence alignment. Comput Appl Biosci 11, 13–18.
    PubMed CAS Google Scholar
27. Vingron, M., and Argos, P. (1989) A fast and sensitive multiple sequence alignment algorithm. Comput Appl Biosci 5, 115–21.
    PubMed CAS Google Scholar
28. Gotoh, O. (1990) Consistency of optimal sequence alignments. Bull Math Biol 52, 509–25.
    PubMed CAS Google Scholar
29. Notredame, C., Holm, L., and Higgins, D. G. (1998) COFFEE: an objective function for multiple sequence alignments. Bioinformatics 14, 407–22.
    Article PubMed CAS Google Scholar
30. Notredame, C., Higgins, D. G., and Heringa, J. (2000) T-coffee: a novel method for fast and accurate multiple sequence alignment. J Mol Biol 302, 205–17.
    Article PubMed CAS Google Scholar
31. Higgins, D. G., and Sharp, P. M. (1988) CLUSTAL: a package for performing multiple sequence alignment on a microcomputer. Gene 73, 237–44.
    Article PubMed CAS Google Scholar
32. Jones, D. T., Taylor, W. R., and Thornton, J. M. (1992) The rapid generation of mutation data matrices from protein sequences. Comput Appl Biosci 8, 275–82.
    PubMed CAS Google Scholar
33. Altschul, S. F. (1998) Generalized affine gap costs for protein sequence alignment. Proteins 32, 88–96.
    Article PubMed CAS Google Scholar
34. Myers, E. W., and Miller, W. (1988) Optimal alignments in linear space. Comput Appl Biosci 4, 11–17.
    PubMed CAS Google Scholar
35. Gribskov, M., McLachlan, A. D., and Eisenberg, D. (1987) Profile analysis: detection of distantly related proteins. Proc Natl Acad Sci USA, 84, 4355–58.
    Article PubMed CAS Google Scholar
36. Schwartz, S., Kent, W. J., Smit, A., Zhang, Z., Baertsch, R., Hardison, R. C., Haussler, D., and Miller, W. (2003) Human-mouse alignments with BLASTZ. Genome Res 13, 103–7.
    Article PubMed CAS Google Scholar
37. http://genome.ucsc.edu/FAQ/FAQformat
38. http://genome.ucsc.edu/
39. Smit, A. F. A., Hubley, R., and Green, P. Repeatmasker. http://www.repeatmasker.org/
40. Benson, G. (1999) Tandem repeats finder: a program to analyze DNA sequences. Nucleic Acids Res 27, 573–80.
    Article PubMed CAS Google Scholar
41. http://globin.cse.psu.edu/dist/gmaj/
42. http://www.bx.psu.edu/miller_lab/dist/tba_howto.pdf
43. http://gel.ahabs.wisc.edu/mauve/mauve-user-guide/
44. Altschul, S. F., Madden, T. L., Schaffer, A. A., Zhang, J., Zhang, Z., Miller, W., and Lipman, D. J. (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search pro grams. Nucleic Acids Res 25, 3389–402.
    Article PubMed CAS Google Scholar
45. Morgenstern, B., Goel, S., Sczyrba, A., and Dress, A. (2003) Altavist: comparing alternative multiple sequence alignments. Bioinformatics 19, 425–6.
    Article PubMed CAS Google Scholar
46. Lassmann, T., and Sonnhammer, E. L. (2007) Automatic extraction of reliable regions from multiple sequence alignments. BMC Bioinformat 8 Suppl 5, S9.
    Article Google Scholar
47. Morgenstern, B., Dress, A., and Werner, T. (1996) Multiple DNA and protein sequence alignment based on segment-to-segment comparison. Proc Natl Acad Sci USA 93, 12098–103.
    Article PubMed CAS Google Scholar
48. Edgar, R. C. (2004) MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res 32, 1792–7.
    Article PubMed CAS Google Scholar
49. Do, C. B., Mahabhashyam, M. S., Brudno, M., and Batzoglou, S. (2005) ProbCons: probabilistic consistency-based multiple sequence alignment. Genome Res 15, 330–40.
    Article PubMed CAS Google Scholar
50. Lassmann, T., and Sonnhammer, E. L. (2005) Kalign – an accurate and fast multiple sequence alignment algorithm. BMC Bioinformat 6, 298.
    Article Google Scholar
51. Wallace, I. M., O’Sullivan, O., Higgins, D. G., and Notredame, C. (2006) M-Coffee: combining multiple sequence alignment methods with t-coffee. Nucleic Acids Res 34, 1692–9.
    Article PubMed CAS Google Scholar
52. Golubchik, T., Wise, M. J., Easteal, S., and Jermiin, L. S. (2007) Mind the gaps: Evidence of bias in estimates of multiple sequence alignments. Mol Biol Evol 24, 2433–42.
    Google Scholar
53. Do, C. B., and Katoh, K. (2008) Protein multiple sequence alignment Functional Proteomics, Methods Mol Biol 484, 379–413.
    Google Scholar
54. Morrison, D. (2006) Multiple sequence alignment for phylogenetic purposes. Aust Syst Bot 19, 479–539.
    Article CAS Google Scholar
55. Roshan, U., and Livesay, D. R. (2006) Probalign: multiple sequence alignment using partition function posterior probabilities. Bioinformatics 22, 2715–21.
    Article PubMed CAS Google Scholar
56. Yamada, S., Gotoh, O., and Yamana, H. (2006) Improvement in accuracy of multiple sequence alignment using novel group-to-group sequence alignment algorithm with piecewise linear gap cost. BMC Bioinformat 7, 524.
    Article Google Scholar
57. Brudno, M., Do, C. B., Cooper, G. M., Kim, M. F., Davydov, E., Green, E. D., Sidow, A., and Batzoglou, S. (2003) LAGAN and multi-LAGAN: efficient tools for large-scale multiple alignment of genomic DNA. Genome Res 13, 721–31.
    Article PubMed CAS Google Scholar
58. Bray, N., and Pachter, L. (2004) MAVID: constrained ancestral alignment of multiple sequences. Genome Res. 14, 693–9.
    Article PubMed CAS Google Scholar

Download references