Fig. 1

Comparing the performance of TrawlerWeb with other web-based motif discovery tools. a Duration of 11 independent runs for TrawlerWeb (blue), RSAT peak-motifs (green) and MEME-ChIP (red) in minutes. The mean is represented by the horizontal line for each dataset. The error bars indicate the standard deviation from the mean. The data are ordered by increasing size of the FASTA input file from left to right. Note that MEME-ChIP did not find any motifs for Dr, hence the motif discovered by DREME was used (see also Fig. 2a). b Overall performance benchmark of TrawlerWeb against 7 other algorithms, using 65 ChIP pulled down experiments on yeast dataset from [38]. MEME-c: MEME algorithm run on conserved regions only. c Comparison of percentage occurrence of over-represented motifs across test datasets. Motif discovery were conducted using 4 algorithms (DREME, MEME, RSAT peak-motifs, and TrawlerWeb) on the test datasets and the number of sequences containing the highest scoring motif were expressed as a percentage of the total number of analysed input sequences. The MEME-ChIP pipeline uses both MEME and DREME motif discovery tools for finding relatively long and short motifs respectively. The MEME algorithm uses a random subsample of 600 sequences. Dr = Danio rerio, At = Arabidopsis thaliana, Mm = Mus musculus, Dm = Drosophila melanogaster, Hs = Homo sapiens