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Identifying DNA and protein patterns with statistically significant alignments of multiple sequences
A greedy algorithm for determining alignments of functionally related sequences is described, and the accuracy of the P value calculations are tested, and an example of using the algorithm to identify binding sites for the Escherichia coli CRP protein is given.
An improved map of conserved regulatory sites for Saccharomyces cerevisiae
- K. MacIsaac, Ting Wang, D. B. Gordon, D. Gifford, G. Stormo, E. Fraenkel
- BiologyBMC Bioinformatics
- 1 March 2006
Improved versions of two conservation-based motif discovery algorithms, PhyloCon and Converge, are reported, which improve the ability to identify the specificity of transcriptional regulators from genome-wide chromatin immunoprecipitation data.
DNA binding sites: representation and discovery
- G. Stormo
The purpose of this article is to provide a brief history of the development and application of computer algorithms for the analysis and prediction of DNA binding sites. This problem can be…
Information content of binding sites on nucleotide sequences.
The AP-1 transcription factor Batf controls TH17 differentiation
It is shown that Batf is required for the differentiation of IL17-producing T helper (TH17) cells, and it is demonstrated that the AP-1 protein BATF has a critical role in TH17 differentiation.
Comparative Genomics Identifies a Flagellar and Basal Body Proteome that Includes the BBS5 Human Disease Gene
Analysis of Homeodomain Specificities Allows the Family-wide Prediction of Preferred Recognition Sites
Splicing signals in Drosophila: intron size, information content, and consensus sequences.
- S. Mount, C. Burks, G. Hertz, G. Stormo, O. White, C. Fields
- BiologyNucleic acids research
- 25 August 1992
A database of 209 Drosophila introns was extracted from Genbank and examined by a number of methods in order to characterize features that might serve as signals for messenger RNA splicing and found that there is a discontinuity in A + T content between exons and introns, which are A +T rich.
The Neuropeptide Pigment-Dispersing Factor Coordinates Pacemaker Interactions in the Drosophila Circadian System
Time-series immunostainings for the PERIOD protein in normal and pdf mutant flies over 9 d of constant conditions suggest that pdf is not required to maintain circadian protein oscillations under constant conditions; however, it is required to coordinate the phase and amplitude of such rhythms among the diverse pacemakers.
Use of the 'Perceptron' algorithm to distinguish translational initiation sites in E. coli.
- G. Stormo, T. D. Schneider, L. Gold, A. Ehrenfeucht
- Biology, Computer ScienceNucleic acids research
- 11 May 1982
We have used a "Perceptron" algorithm to find a weighting function which distinguishes E. coli translational initiation sites from all other sites in a library of over 78,000 nucleotides of mRNA…