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- person_outline Keith Robison
Publication for DPInteract
Cis regulatory motifs and antisense transcriptional control in the apicomplexan Theileria parva
[…] c motif databases JASPAR  and TRANSFAC , FLY , FlyReg  and Agris , AthaMap , PLACE , Uniprobe , other yeast motifs [, ], as well as the prokaryotic motif databases RegTransBase  and DPInteract . The Smith-Waterman local alignment method with a similarity score defined by Pearson’s correlation coefficient estimated motif similarity. The STAMP motif phylogenetic tree was generate […]
Strikingly Bacteria Like and Gene Rich Mitochondrial Genomes throughout Jakobid Protists
[…] of 200) of potential sites per genome, instead of 0 or >1,000, obtained with other tools tested. BPROM searches for sequence motifs derived from validated bacterial functional sites collected in the DPInteract database (). The algorithm of promoter identification is based on linear discriminant function that accounts for sequence characteristics of promoter regions. Because the score is a logarit […]
Using Sequence Specific Chemical and Structural Properties of DNA to Predict Transcription Factor Binding Sites
[…] binding sites. We randomly selected 10,000 non-coding sequences to serve as negative examples for each TF, and mapped these sequences to feature vectors. We also obtained positive training data from DPInteract . The source of training data did not affect the main qualitative findings of our method comparisons reported in the section. Namely, we find that the performance of SiteSleuth is better t […]
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