pmc logo image
Logo of pnasPNAS Home page.Reference to the article.PNAS Info for AuthorsPNAS SubscriptionsPNAS About
Journal List > Proc Natl Acad Sci U S A > v.86(12); Jun 1989

Formats:
Proc Natl Acad Sci U S A. 1989 June; 86(12): 4412–4415.
PMCID: PMC287279
Copyright notice
A tool for multiple sequence alignment.
D J Lipman, S F Altschul, and J D Kececioglu
Mathematical Research Branch, National Institute of Diabetes and Digestive and Kidney Diseases, Bethesda, MD 20894.
Small right arrow pointing to: This article has been cited by other articles in PMC.
Abstract
Multiple sequence alignment can be a useful technique for studying molecular evolution and analyzing sequence-structure relationships. Until recently, it has been impractical to apply dynamic programming, the most widely accepted method for producing pairwise alignments, to comparisons of more than three sequences. We describe the design and application of a tool for multiple alignment of amino acid sequences that implements a new algorithm that greatly reduces the computational demands of dynamic programming. This tool is able to align in reasonable time as many as eight sequences the length of an average protein.
Full text
Full text is available as a scanned copy of the original print version. Get a printable copy (PDF file) of the complete article (813K), or click on a page image below to browse page by page. Links to PubMed are also available for Selected References.
 
icon of scanned page 4412
4412
icon of scanned page 4413
4413
icon of scanned page 4414
4414
icon of scanned page 4415
4415
 
Selected References
These references are in PubMed. This may not be the complete list of references from this article.
  • Trifonov EN, Bolshoi G. Open and closed 5 S ribosomal RNA, the only two universal structures encoded in the nucleotide sequences. J Mol Biol. 1983 Sep 5;169(1):1–13. [PubMed]
  • Galas DJ, Eggert M, Waterman MS. Rigorous pattern-recognition methods for DNA sequences. Analysis of promoter sequences from Escherichia coli. J Mol Biol. 1985 Nov 5;186(1):117–128. [PubMed]
  • Wu TT, Kabat EA. An analysis of the sequences of the variable regions of Bence Jones proteins and myeloma light chains and their implications for antibody complementarity. J Exp Med. 1970 Aug 1;132(2):211–250. [PubMed]
  • Wilbur WJ, Lipman DJ. Rapid similarity searches of nucleic acid and protein data banks. Proc Natl Acad Sci U S A. 1983 Feb;80(3):726–730. [PubMed]
  • Lipman DJ, Pearson WR. Rapid and sensitive protein similarity searches. Science. 1985 Mar 22;227(4693):1435–1441. [PubMed]
  • Fitch WM. Further improvements in the method of testing for evolutionary homology among proteins. J Mol Biol. 1970 Apr 14;49(1):1–14. [PubMed]
  • Bacon DJ, Anderson WF. Multiple sequence alignment. J Mol Biol. 1986 Sep 20;191(2):153–161. [PubMed]
  • Bashford D, Chothia C, Lesk AM. Determinants of a protein fold. Unique features of the globin amino acid sequences. J Mol Biol. 1987 Jul 5;196(1):199–216. [PubMed]
  • Needleman SB, Wunsch CD. A general method applicable to the search for similarities in the amino acid sequence of two proteins. J Mol Biol. 1970 Mar;48(3):443–453. [PubMed]
  • Gotoh O. Alignment of three biological sequences with an efficient traceback procedure. J Theor Biol. 1986 Aug 7;121(3):327–337. [PubMed]
  • Johnson MS, Doolittle RF. A method for the simultaneous alignment of three or more amino acid sequences. J Mol Evol. 1986;23(3):267–278. [PubMed]
  • Sobel E, Martinez HM. A multiple sequence alignment program. Nucleic Acids Res. 1986 Jan 10;14(1):363–374. [PubMed]
  • Feng DF, Doolittle RF. Progressive sequence alignment as a prerequisite to correct phylogenetic trees. J Mol Evol. 1987;25(4):351–360. [PubMed]
  • Sahota A, Ranjekar PK, Alfonzo J, Lewin AS, Taylor MW. Mutants of Saccharomyces cerevisiae deficient in adenine phosphoribosyltransferase. Mutat Res. 1987 Sep;180(1):81–87. [PubMed]
  • Taylor WR. Identification of protein sequence homology by consensus template alignment. J Mol Biol. 1986 Mar 20;188(2):233–258. [PubMed]
  • Fitch Walter M, Smith Temple F. Optimal sequence alignments. Proc Natl Acad Sci U S A. 1983 Mar;80(5):1382–1386. [PubMed]
  • Gotoh O. An improved algorithm for matching biological sequences. J Mol Biol. 1982 Dec 15;162(3):705–708. [PubMed]
  • Altschul SF, Erickson BW. Optimal sequence alignment using affine gap costs. Bull Math Biol. 1986;48(5-6):603–616. [PubMed]
  • Myers EW, Miller W. Optimal alignments in linear space. Comput Appl Biosci. 1988 Mar;4(1):11–17. [PubMed]
  • Saitou N, Nei M. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol. 1987 Jul;4(4):406–425. [PubMed]
  • Greer J. Comparative model-building of the mammalian serine proteases. J Mol Biol. 1981 Dec 25;153(4):1027–1042. [PubMed]
  • Bajaj M, Blundell T. Evolution and the tertiary structure of proteins. Annu Rev Biophys Bioeng. 1984;13:453–492. [PubMed]
Articles from Proceedings of the National Academy of Sciences of the United States of America are provided here courtesy of
National Academy of Sciences

PubMed articles by these authors