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PMID: 15511292 Published · epublish English Comparative Study Journal Article Research Support, Non-U.S. Gov't Research Support, U.S. Gov't, Non-P.H.S. Research Support, U.S. Gov't, P.H.S.

PhyME: a probabilistic algorithm for finding motifs in sets of orthologous sequences.

BMC bioinformatics ·Vol. 5 ·2004-10-28 ·Pages 170

Sinha S, Blanchette M, Tompa M

Abstract

This paper addresses the problem of discovering transcription factor binding sites in heterogeneous sequence data, which includes regulatory sequences of one or more genes, as well as their orthologs in other species. We propose an algorithm that integrates two important aspects of a motif's significance - overrepresentation and cross-species conservation - into one probabilistic score. The algorithm allows the input orthologous sequences to be related by any user-specified phylogenetic tree. It is based on the Expectation-Maximization technique, and scales well with the number of species and the length of input sequences. We evaluate the algorithm on synthetic data, and also present results for data sets from yeast, fly, and human. The results demonstrate that the new approach improves motif discovery by exploiting multiple species information.

MeSH Terms
Algorithms Animals Base Composition/genetics DNA/genetics DNA, Fungal/genetics Drosophila/genetics Drosophila melanogaster/genetics Enhancer Elements, Genetic/genetics Evolution, Molecular Humans Models, Genetic Phylogeny Saccharomyces/genetics Saccharomyces cerevisiae/genetics Software Species Specificity
Chemicals
DNA, Fungal DNA
Authors & Affiliations
3 authors, click to expand affiliations / ORCID
Sinha Saurabh
Center for Studies in Physics and Biology, The Rockefeller University, New York, NY 10021, USA. [email protected]
Blanchette Mathieu
Tompa Martin
References (27)
27 references, click to expand
  1. SCPD: a promoter database of the yeast Saccharomyces cerevisiae.
    Bioinformatics. 1999 Jul-Aug;15(7-8):607-11 PMID: 10487868
  2. Prediction of transcription regulatory sites in Archaea by a comparative genomic approach.
    Nucleic Acids Res. 2000 Feb 1;28(3):695-705 PMID: 10637320
  3. Conservation of DNA regulatory motifs and discovery of new motifs in microbial genomes.
    Genome Res. 2000 Jun;10(6):744-57 PMID: 10854408
  4. Surveying Saccharomyces genomes to identify functional elements by comparative DNA sequence analysis.
    Genome Res. 2001 Jul;11(7):1175-86 PMID: 11435399
  5. Identification of a novel cis-regulatory element involved in the heat shock response in Caenorhabditis elegans using microarray gene expression and computational methods.
    Genome Res. 2002 May;12(5):701-12 PMID: 11997337
  6. Discovery of regulatory elements by a computational method for phylogenetic footprinting.
    Genome Res. 2002 May;12(5):739-48 PMID: 11997340
  7. rVista for comparative sequence-based discovery of functional transcription factor binding sites.
    Genome Res. 2002 May;12(5):832-9 PMID: 11997350
  8. Computational detection of genomic cis-regulatory modules applied to body patterning in the early Drosophila embryo.
    BMC Bioinformatics. 2002 Oct 24;3:30 PMID: 12398796
  9. Finishing a whole-genome shotgun: release 3 of the Drosophila melanogaster euchromatic genome sequence.
    Genome Biol. 2002;3(12):RESEARCH0079 PMID: 12537568
  10. LAGAN and Multi-LAGAN: efficient tools for large-scale multiple alignment of genomic DNA.
    Genome Res. 2003 Apr;13(4):721-31 PMID: 12654723
  11. Sequencing and comparison of yeast species to identify genes and regulatory elements.
    Nature. 2003 May 15;423(6937):241-54 PMID: 12748633
  12. Gibbs Recursive Sampler: finding transcription factor binding sites.
    Nucleic Acids Res. 2003 Jul 1;31(13):3580-5 PMID: 12824370
  13. Regulatory sequence analysis tools.
    Nucleic Acids Res. 2003 Jul 1;31(13):3593-6 PMID: 12824373
  14. A probabilistic method to detect regulatory modules.
    Bioinformatics. 2003;19 Suppl 1:i292-301 PMID: 12855472
  15. Conservation of regulatory elements between two species of Drosophila.
    BMC Bioinformatics. 2003 Nov 20;4:57 PMID: 14629780
  16. Combining phylogenetic data with co-regulated genes to identify regulatory motifs.
    Bioinformatics. 2003 Dec 12;19(18):2369-80 PMID: 14668220
  17. Phylogenetic motif detection by expectation-maximization on evolutionary mixtures.
    Pac Symp Biocomput. 2004;:324-35 PMID: 14992514
  18. Motif discovery in heterogeneous sequence data.
    Pac Symp Biocomput. 2004;:348-59 PMID: 14992516
  19. Eukaryotic regulatory element conservation analysis and identification using comparative genomics.
    Genome Res. 2004 Mar;14(3):451-8 PMID: 14993210
  20. Aligning multiple genomic sequences with the threaded blockset aligner.
    Genome Res. 2004 Apr;14(4):708-15 PMID: 15060014
  21. Identification of consensus patterns in unaligned DNA sequences known to be functionally related.
    Comput Appl Biosci. 1990 Apr;6(2):81-92 PMID: 2193692
  22. Evolutionary trees from DNA sequences: a maximum likelihood approach.
    J Mol Evol. 1981;17(6):368-76 PMID: 7288891
  23. fastDNAmL: a tool for construction of phylogenetic trees of DNA sequences using maximum likelihood.
    Comput Appl Biosci. 1994 Feb;10(1):41-8 PMID: 8193955
  24. Detecting subtle sequence signals: a Gibbs sampling strategy for multiple alignment.
    Science. 1993 Oct 8;262(5131):208-14 PMID: 8211139
  25. TRANSFAC: a database on transcription factors and their DNA binding sites.
    Nucleic Acids Res. 1996 Jan 1;24(1):238-41 PMID: 8594589
  26. Extracting regulatory sites from the upstream region of yeast genes by computational analysis of oligonucleotide frequencies.
    J Mol Biol. 1998 Sep 4;281(5):827-42 PMID: 9719638
  27. Finding DNA regulatory motifs within unaligned noncoding sequences clustered by whole-genome mRNA quantitation.
    Nat Biotechnol. 1998 Oct;16(10):939-45 PMID: 9788350
Article Info
Journal
BMC bioinformatics
Abbr.
BMC Bioinformatics
ISSN
1471-2105
DOI
10.1186/1471-2105-5-170
Email
[email protected]
Published
2004-10-28
Epub
2004-00-28
Pages
170
Language
English
Region
England
NLM ID
100965194
PMCID
PMC534098
Subset
IM
Grants
NHGRI NIH HHS · R01 HG002602 · United States
NHGRI NIH HHS · R01 HG02602 · United States
External Links
PubMed source DOI: 10.1186/1471-2105-5-170 PMC Full Text View journal details
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