Consensus patterns in DNA
- PMID: 2179676
- DOI: 10.1016/0076-6879(90)83015-2
Consensus patterns in DNA
Abstract
Matrices can provide realistic representations of protein/DNA specificity. In many cases simple mononucleotide-based matrices are adequate representations, but more complex matrices may be needed for other cases. Unlike simple consensus sequences, matrices allow for different penalties to be assessed for different changes to a binding site, a property that is essential for accurate description of a binding site pattern. When only a collection of binding site sequences is known, the best representation for the pattern is an information content formulation, based on both thermodynamic and statistical considerations. Quantitative data on relative binding affinities may be used to determine matrices that provide a best fit to the data. Matrix representations also provide an efficient method of aligning multiple sequences to identify binding site patterns that they have in common.
Similar articles
-
Identification of consensus patterns in unaligned DNA sequences known to be functionally related.Comput Appl Biosci. 1990 Apr;6(2):81-92. doi: 10.1093/bioinformatics/6.2.81. Comput Appl Biosci. 1990. PMID: 2193692
-
Escherichia coli promoter sequences: analysis and prediction.Methods Enzymol. 1996;273:30-42. doi: 10.1016/s0076-6879(96)73004-5. Methods Enzymol. 1996. PMID: 8791597 Review. No abstract available.
-
Rigorous pattern-recognition methods for DNA sequences. Analysis of promoter sequences from Escherichia coli.J Mol Biol. 1985 Nov 5;186(1):117-28. doi: 10.1016/0022-2836(85)90262-1. J Mol Biol. 1985. PMID: 3908689
-
Weight matrix descriptions of four eukaryotic RNA polymerase II promoter elements derived from 502 unrelated promoter sequences.J Mol Biol. 1990 Apr 20;212(4):563-78. doi: 10.1016/0022-2836(90)90223-9. J Mol Biol. 1990. PMID: 2329577
-
Compilation and analysis of Escherichia coli promoter DNA sequences.Nucleic Acids Res. 1983 Apr 25;11(8):2237-55. doi: 10.1093/nar/11.8.2237. Nucleic Acids Res. 1983. PMID: 6344016 Free PMC article. Review.
Cited by
-
Evaluation of methods for modeling transcription factor sequence specificity.Nat Biotechnol. 2013 Feb;31(2):126-34. doi: 10.1038/nbt.2486. Epub 2013 Jan 27. Nat Biotechnol. 2013. PMID: 23354101 Free PMC article.
-
Specificity of the Mnt protein determined by binding to randomized operators.Proc Natl Acad Sci U S A. 1991 Jul 1;88(13):5699-703. doi: 10.1073/pnas.88.13.5699. Proc Natl Acad Sci U S A. 1991. PMID: 2062848 Free PMC article.
-
Additivity in protein-DNA interactions: how good an approximation is it?Nucleic Acids Res. 2002 Oct 15;30(20):4442-51. doi: 10.1093/nar/gkf578. Nucleic Acids Res. 2002. PMID: 12384591 Free PMC article.
-
Computational gene finding in plants.Plant Mol Biol. 2002 Jan;48(1-2):39-48. Plant Mol Biol. 2002. PMID: 11860211 Review.
-
Feature selection for the prediction of translation initiation sites.Genomics Proteomics Bioinformatics. 2005 May;3(2):73-83. doi: 10.1016/s1672-0229(05)03012-3. Genomics Proteomics Bioinformatics. 2005. PMID: 16393144 Free PMC article.
Publication types
MeSH terms
Substances
Grants and funding
LinkOut - more resources
Full Text Sources