Multiple sequence alignment

Suggested reading

Reviews

  1. Mount, Chapt. 4, 139-160
  2. Dummies, Chapt. 9.
  3. Bauxevanis and Ouellette, Chapter 8
  4. Thompson, J. D., Plewniak, F., and Poch, O. (1999) A comprehensive comparison of multiple sequence alignment programs. Nucleic Acids Res 27:2682-2690. [Entrez]

Theory

  1. Chan, S. C., Wong, A. K. C., and Chiu, D. K. Y. (1992) A survey of multiple sequence comparison methods. Bull. Math. Biol. 54:563-598.[Entrez]
  2. Carrillo, H. and Lipman, D. J. (1988) The multiple sequence alignment problem in biology. SIAM J. Appl. Math. 48:1073-1082.
  3. Altschul, S. F. and Lipman, D. J. (1989) Trees, stars, and multiple biological sequence alignment. SIAM J. Appl. Math. 49:197-209.
  4. Altschul, S. F. (1989) Gap costs and multiple alignment. J. Theor. Biol. 138:297-309. [Entrez]
  5. Lipman, D. J., Altschul, S. F., and Kececioglu, J. D. (1989) A tool for multiple sequence alignment. Proc. Natl. Acad. Sci. USA 86:4412-5. [Entrez]

Clustal/T-Coffee

  1. Higgins, D. G. and Sharp, P. M. (1988) CLUSTAL: a package for performing multiple sequence alignment on a microcomputer. Gene 73:237-244. [Entrez]
  2. 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 22:4673-4680. [Entrez]

    ClustalW on the Web: http://www2.ebi.ac.uk/clustalw

  3. Notredame C., Higgins D. G., Heringa J. (2000) "T-Coffee: A novel method for fast and accurate multiple sequence alignment." J. Mol. Biol. 302:205-17 [Entrez]
  4. R. C. Edgar (2004) MUSCLE: multiple sequence alignment with high accuracy and high throughput Nuc. Acids. Res. 19:1792 [Entrez]

Treealign -

  1. Hein, J., "Unified approach to alignment and phylogenies", Meth. Enzymol., 1990 , 626-645. [Entrez]

Progressive Alignment -

  1. Feng, D. and Doolittle, R. F. (1987) Progressive sequence alignment as a prerequisite to correct phylogenetic trees. J. Mol. Evol. 25:351-360. [Entrez]
  2. Feng, D. and Doolittle, R. F. (1990) Progressive alignment and phylogentic tree construction of protein sequences. Methods Enzymol. 183:375-387. [Entrez]

Other pairwise approaches -

  1. Taylor, W. R. (1988) A flexible method to align large numbers of biological sequences. J. Mol. Evol. 28:161-169. [Entrez]
  2. Barton, G. J. (1990) Protein multiple sequence alignment and flexible pattern matching. Methods Enzymol. 183:403-428. [Entrez]

Other approaches -

  1. Bacon, D. J. and Anderson, W. F. (1986) Multiple sequence alignment. J. Mol. Biol. 191:153-161. [Entrez]
  2. Schuler, G. D., Altschul, S. F., and Lipman, D. J. (1991) A workbench for multiple alignment construction and analysis. PROTEINS 9:180-190. (MACAW) [Entrez]

Multiple alignment WWW pages

http://www.people.virginia.edu/~wrp/cshl99/mult-res.html

BCM Search Launcher: Multiple Sequence Alignment. http://dot.imgen.bcm.tmc.edu:9331/multi-align/multi-align.html

VSNS Biocomputing Division Multiple Alignment Resource Page: http://www.techfak.uni-bielefeld.de/bcd/Curric/MulAli/welcome.html
-- Provides an extensive list of multiple alignment resources, including lists of multiple lignment servers, analysis programs, alignment editors, on-line tutorials, etc.

MAP (Multiple Alignment Program) http://genome.cs.mtu.edu/map.html

Multiple Alignment Exercises

http://www.people.virginia.edu/~wrp/cshl99/smith_ex.html

Bioch508 home page

wrp@virginia.edu