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Publication for ScerTF
Developmentally regulated internal transcription initiation during meiosis in budding yeast
[…] then performed on these sequences using the Motif module from the Biopython libraries (http://biopython.org) with the Position Weight Matrix (PWM) of the Ndt80 or Ime1 binding profile retrieved from ScerTF  (http://stormo.wustl.edu/ScerTF/). Sequences 300 nt upstream to each ORF served as negative control. Sites with a PWM score larger than 85% of the possible score range were classified as pot […]
ChEC seq kinetics discriminates transcription factor binding sites by DNA sequence and shape in vivo
[…] taFromBed. FASTA sequences were then scored using a custom perl script (pssm_scorer.pl in ) implementing the FIMO algorithm and using previously determined position frequency matrices downloaded from ScerTF. FASTA sequences were uploaded to the MEME-ChIP web server for de novo motif discovery. Logos were generated with LogOddsLogo, using the yeast GC content option. […]
Contribution of Sequence Motif, Chromatin State, and DNA Structure Features to Predictive Models of Transcription Factor Binding in Yeast
[…] avoid over fitting. Because we are interested in dissecting the relative contributions of SM, CS, and DS features, we could only focus on 40 TFs with annotated sequence motif information in both the ScerTF database  and in the ChIP-chip dataset . An additional 161 TFs for which sequence motifs are not available (i.e. not in ScerTF or less than 30 bound probes in the ChIP-chip dataset) were us […]
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