Additional file 5 of Evaluating tools for transcription factor binding site prediction

Evaluation of search tools using PWMs generated from the ENCODE-ChIP-Seq data using rGADEM. Sensitivity, Positive predictive value, Geometric accuracy and False positive rate for the 12 TFBSs that are found in the PAZAR-E dataset. Separate sheets are provided for each of the search tools. (XLS 29.5 kb

Additional file 4 of Evaluating tools for transcription factor binding site prediction

Sequence Logos. Sequence logos for the first PWM generated for the 12 TFBSs using each of the four motif discovery tools. (PDF 29.5 kb

Additional file 1 of Evaluating tools for transcription factor binding site prediction

The PAZAR Reference Dataset. Entries from PAZAR, with the numbers of each TFBS that they contain. The spreadsheet also indicates whether the TFBSs are found in JASPAR and/or the ENCODE-ChIP-Seq data. (XLS 54 kb

Additional file 2 of Evaluating tools for transcription factor binding site prediction

Evaluation of search tools using JASPAR.2010 PWMs. Sensitivity, Positive predictive value, Geometric accuracy and False positive rate for the 14 TFBSs that are found in the PAZAR-J dataset. Separate sheets are provided for each of the search tools. (XLS 31.5 kb