Additional file 1: of TrawlerWeb: an online de novo motif discovery tool for next-generation sequencing datasets

Table S1. Details of the assessment of TrawlerWeb. Detailed table of Fig. 1b showing, for each ChIP experiment, the ability of individual programs to uncover the correct binding site in yeast. For each individual ChIP experiment, the success or failure of 8 different algorithms including TrawlerWeb is shown. The results from the 6 algorithms (Coverage, AlignACE, Kellis, mdscan, MEME, and MEME-c) were extracted from Harbison et al. 2004 [38]. The matching motifs found by TrawlerWeb are identical to that found by Trawler_standalone (detailed previously in Ettwiller et al. 2007 [5]). The results from RSAT were performed by this study, where the matching motifs found by RSAT were described in the last column. (XLSX 190 kb

Additional file 2: of TrawlerWeb: an online de novo motif discovery tool for next-generation sequencing datasets

Table S2. Details of motif occurrence comparison between web-based motif discovery software. The highest scoring motifs discovered in DREME, MEME, RSAT peak-motifs, and TrawlerWeb and their corresponding occurrences are illustrated here. For the highest scoring motif, the number of motif occurrences were expressed as a percentage of the total number of input sequences. *MEME-ChIP pre-processes submitted sequences longer than 100 by trimming them evenly from both ends to get the centered 100 bp sequence and discards trimmed sequences containing only Ns from repeat masking. **MEME motif discovery automatically limits the run to a randomly sampled 600 sequences to reduce run time. (XLSX 576 kb