Discovering novel sequence motifs with MEME.
DOI: 10.1002/0471250953.BI0204S00
关键词: Sequence pattern 、 Consensus sequence 、 Motif (music) 、 Biology 、 Computational biology 、 Data mining 、 Training set 、 Sequence motif 、 Multiple EM for Motif Elicitation
摘要: This unit illustrates how to use MEME discover motifs in a group of related nucleotide or peptide sequences. A motif is sequence pattern that occurs repeatedly one more sequences the input group. can be used novel patterns because it bases its discoveries only on sequences, not any prior knowledge (such as databases known motifs). The set unaligned same type (peptide nucleotide). For each discovers, reports occurrences (sites), consensus sequence, and level conservation (information content) at position pattern. also produces block diagrams showing where all discovered occur training MEME's hypertext (HTML) output contains buttons allow for convenient other searches.
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core.ac.uk参考文章(7)
S Pietrokovski, Searching databases of conserved sequence regions by aligning protein multiple-alignments Nucleic Acids Research. ,vol. 24, pp. 3836- 3845 ,(1996) , 10.1093/NAR/24.19.3836
Jack Kyte, Russell F. Doolittle, A simple method for displaying the hydropathic character of a protein Journal of Molecular Biology. ,vol. 157, pp. 105- 132 ,(1982) , 10.1016/0022-2836(82)90515-0
J. van Helden, B. André, J. Collado-Vides, Extracting Regulatory Sites from the Upstream Region of Yeast Genes by Computational Analysis of Oligonucleotide Frequencies Journal of Molecular Biology. ,vol. 281, pp. 827- 842 ,(1998) , 10.1006/JMBI.1998.1947
Charles E. Lawrence, Andrew A. Reilly, An expectation maximization (EM) algorithm for the identification and characterization of common sites in unaligned biopolymer sequences. Proteins. ,vol. 7, pp. 41- 51 ,(1990) , 10.1002/PROT.340070105
Shmuel Pietrokovski, Jorja G Henikoff, Steven Henikoff, The Blocks Database—A System for Protein Classification Nucleic Acids Research. ,vol. 24, pp. 197- 200 ,(1996) , 10.1093/NAR/24.1.197
T. L. Bailey, M. Gribskov, Combining evidence using p-values: application to sequence homology searches. Bioinformatics. ,vol. 14, pp. 48- 54 ,(1998) , 10.1093/BIOINFORMATICS/14.1.48
Edgar Wingender, Xin Chen, Reinhard Hehl, Holger Karas, Ines Liebich, Volker Matys, T Meinhardt, M Prüß, Ingmar Reuter, Frank Schacherer, TRANSFAC: an integrated system for gene expression regulation Nucleic Acids Research. ,vol. 28, pp. 316- 319 ,(2000) , 10.1093/NAR/28.1.316