Using hexamers to predict cis-regulatory motifs in Drosophila

Bob Y Chan and Dennis Kibler

School of Information and Computer Science, University of California, Irvine, Irvine, California, USA

author email corresponding author email

BMC Bioinformatics 2005, 6:262doi:10.1186/1471-2105-6-262


Published:	27 October 2005

Additional files

Additional File 1:

Sequences comprising the data set. FASTA-formatted sequences that include the 20 kb upstream and downstream of the 16 gap and pair-rule genes that were studied. Sequences were extracted from Release 4.1 of the Drosophila genome using FlyBase's "GBrowse" Genome Browser.

Format: TXT Size: 708KB Download file

Additional File 2:

Coordinates of known CRMs. Coordinates of known CRMs, relative to the sequences in 2.

Format: TXT Size: 2KB Download file

Additional File 3:

Coordinates of CRMs predicted by the different algorithms. Coordinates of predicted CRMs for each of the algorithms compared in this study, relative to the sequences in 2.

Format: TXT Size: 32KB Download file

Additional File 4:

Hd hexamers. Top 80 H_dhexamers calculated by the HexDiff algorithm for each round of cross-validation.

Format: TXT Size: 69KB Download file

Additional File 5:

ROC curves for the HexDiff algorithm. The three curves in this plot were made by taking the combination of parameters that gave the best performance on the training sets (number of nmers: 80, window size: 1700 bp, threshold: 170) and holding two parameters constant while varying the third.

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Additional File 6:

Sensitivities and specificities for HexDiff and the other algorithms. Sensitivities and specificities for HexDiff and the other algorithms were calculated by checking whether each position was a TP, FP, TN, or FN and using the appropriate formulas.

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