Skip to main content
Nucleic Acids Research logoLink to Nucleic Acids Research
. 1992 Mar 11;20(5):1093–1099. doi: 10.1093/nar/20.5.1093

Critical comparison of consensus methods for molecular sequences.

W H Day 1, F R McMorris 1
PMCID: PMC312096  PMID: 1549472

Abstract

Consensus methods are recognized as valuable tools for data analysis, especially when some sort of data aggregation is desired. Although consensus methods for sequences play a vital role in molecular biology, researchers pay little heed to the features and limitations of such methods, and so there are risks that criteria for constructing consensus sequences will be misused or misunderstood. To understand better the issues involved, we conducted a critical comparison of nine consensus methods for sequences, of which eight were used in papers appearing in this journal. We report the results of that comparison, and we make recommendations which we hope will assist researchers when they must select particular consensus methods for particular applications.

Full text

PDF
1098

Selected References

These references are in PubMed. This may not be the complete list of references from this article.

  1. Bains W. MULTAN (2), a multiple string alignment program for nucleic acids and proteins. Comput Appl Biosci. 1989 Feb;5(1):51–52. doi: 10.1093/bioinformatics/5.1.51. [DOI] [PubMed] [Google Scholar]
  2. Bains W. MULTAN: a program to align multiple DNA sequences. Nucleic Acids Res. 1986 Jan 10;14(1):159–177. doi: 10.1093/nar/14.1.159. [DOI] [PMC free article] [PubMed] [Google Scholar]
  3. Card C. O., Wilson G. G., Weule K., Hasapes J., Kiss A., Roberts R. J. Cloning and characterization of the HpaII methylase gene. Nucleic Acids Res. 1990 Mar 25;18(6):1377–1383. doi: 10.1093/nar/18.6.1377. [DOI] [PMC free article] [PubMed] [Google Scholar]
  4. Cavener D. R. Comparison of the consensus sequence flanking translational start sites in Drosophila and vertebrates. Nucleic Acids Res. 1987 Feb 25;15(4):1353–1361. doi: 10.1093/nar/15.4.1353. [DOI] [PMC free article] [PubMed] [Google Scholar]
  5. Cavener D. R., Ray S. C. Eukaryotic start and stop translation sites. Nucleic Acids Res. 1991 Jun 25;19(12):3185–3192. doi: 10.1093/nar/19.12.3185. [DOI] [PMC free article] [PubMed] [Google Scholar]
  6. Choo K. H., Vissel B., Nagy A., Earle E., Kalitsis P. A survey of the genomic distribution of alpha satellite DNA on all the human chromosomes, and derivation of a new consensus sequence. Nucleic Acids Res. 1991 Mar 25;19(6):1179–1182. doi: 10.1093/nar/19.6.1179. [DOI] [PMC free article] [PubMed] [Google Scholar]
  7. Crowther P. J., Doherty J. P., Linsenmeyer M. E., Williamson M. R., Woodcock D. M. Revised genomic consensus for the hypermethylated CpG island region of the human L1 transposon and integration sites of full length L1 elements from recombinant clones made using methylation-tolerant host strains. Nucleic Acids Res. 1991 May 11;19(9):2395–2401. doi: 10.1093/nar/19.9.2395. [DOI] [PMC free article] [PubMed] [Google Scholar]
  8. Daniels G. R., Deininger P. L. Characterization of a third major SINE family of repetitive sequences in the galago genome. Nucleic Acids Res. 1991 Apr 11;19(7):1649–1656. doi: 10.1093/nar/19.7.1649. [DOI] [PMC free article] [PubMed] [Google Scholar]
  9. Gilson E., Saurin W., Perrin D., Bachellier S., Hofnung M. Palindromic units are part of a new bacterial interspersed mosaic element (BIME). Nucleic Acids Res. 1991 Apr 11;19(7):1375–1383. doi: 10.1093/nar/19.7.1375. [DOI] [PMC free article] [PubMed] [Google Scholar]
  10. Grasser K. D., Feix G. Isolation and characterization of maize cDNAs encoding a high mobility group protein displaying a HMG-box. Nucleic Acids Res. 1991 May 25;19(10):2573–2577. doi: 10.1093/nar/19.10.2573. [DOI] [PMC free article] [PubMed] [Google Scholar]
  11. Irwin D. M., Kocher T. D., Wilson A. C. Evolution of the cytochrome b gene of mammals. J Mol Evol. 1991 Feb;32(2):128–144. doi: 10.1007/BF02515385. [DOI] [PubMed] [Google Scholar]
  12. Jurka J., Milosavljevic A. Reconstruction and analysis of human Alu genes. J Mol Evol. 1991 Feb;32(2):105–121. doi: 10.1007/BF02515383. [DOI] [PubMed] [Google Scholar]
  13. Kolodrubetz D. Consensus sequence for HMG1-like DNA binding domains. Nucleic Acids Res. 1990 Sep 25;18(18):5565–5565. doi: 10.1093/nar/18.18.5565. [DOI] [PMC free article] [PubMed] [Google Scholar]
  14. Krinke L., Wulff D. L. The cleavage specificity of RNase III. Nucleic Acids Res. 1990 Aug 25;18(16):4809–4815. doi: 10.1093/nar/18.16.4809. [DOI] [PMC free article] [PubMed] [Google Scholar]
  15. McGeoch D. J. Protein sequence comparisons show that the 'pseudoproteases' encoded by poxviruses and certain retroviruses belong to the deoxyuridine triphosphatase family. Nucleic Acids Res. 1990 Jul 25;18(14):4105–4110. doi: 10.1093/nar/18.14.4105. [DOI] [PMC free article] [PubMed] [Google Scholar]
  16. Piller K. J., Baerson S. R., Polans N. O., Kaufman L. S. Structural analysis of the short length ribosomal DNA variant from Pisum sativum L. cv. Alaska. Nucleic Acids Res. 1990 Jun 11;18(11):3135–3145. doi: 10.1093/nar/18.11.3135. [DOI] [PMC free article] [PubMed] [Google Scholar]
  17. Sakumi K., Shiraishi A., Hayakawa H., Sekiguchi M. Cloning and expresion of cDNA for rat O6-methylguanine-DNA methyltransferase. Nucleic Acids Res. 1991 Oct 25;19(20):5597–5601. doi: 10.1093/nar/19.20.5597. [DOI] [PMC free article] [PubMed] [Google Scholar]
  18. Sayers J. R., Eckstein F. A single-strand specific endonuclease activity copurifies with overexpressed T5 D15 exonuclease. Nucleic Acids Res. 1991 Aug 11;19(15):4127–4132. doi: 10.1093/nar/19.15.4127. [DOI] [PMC free article] [PubMed] [Google Scholar]
  19. Schneider T. D., Stephens R. M. Sequence logos: a new way to display consensus sequences. Nucleic Acids Res. 1990 Oct 25;18(20):6097–6100. doi: 10.1093/nar/18.20.6097. [DOI] [PMC free article] [PubMed] [Google Scholar]
  20. Shapiro M. B., Senapathy P. RNA splice junctions of different classes of eukaryotes: sequence statistics and functional implications in gene expression. Nucleic Acids Res. 1987 Sep 11;15(17):7155–7174. doi: 10.1093/nar/15.17.7155. [DOI] [PMC free article] [PubMed] [Google Scholar]
  21. Waterman M. S., Arratia R., Galas D. J. Pattern recognition in several sequences: consensus and alignment. Bull Math Biol. 1984;46(4):515–527. doi: 10.1007/BF02459500. [DOI] [PubMed] [Google Scholar]
  22. Waterman M. S. Multiple sequence alignment by consensus. Nucleic Acids Res. 1986 Nov 25;14(22):9095–9102. doi: 10.1093/nar/14.22.9095. [DOI] [PMC free article] [PubMed] [Google Scholar]
  23. Yamauchi K. The sequence flanking translational initiation site in protozoa. Nucleic Acids Res. 1991 May 25;19(10):2715–2720. doi: 10.1093/nar/19.10.2715. [DOI] [PMC free article] [PubMed] [Google Scholar]

Articles from Nucleic Acids Research are provided here courtesy of Oxford University Press

RESOURCES