MARS: Motif Assessment and Ranking Suite for transcription factor binding motifs

We describe MARS (Motif Assessment and Ranking Suite), a web-based suite of tools used to evaluate and rank PWM-based motifs. The increased number of learned motif models that are spread across databases and in different PWM formats, leading to a choice dilemma among the users, is our motivation. This increase has been driven by the difficulty of modelling transcription factor binding sites and the advance in high-throughput sequencing technologies at a continually reducing cost. Therefore, several experimental techniques have been developed resulting in diverse motif-finding algorithms and databases. We collate a wide variety of available motifs into a benchmark database, including the corresponding experimental ChIP-seq and PBM data obtained from ENCODE and UniPROBE databases, respectively. The implemented tools include: a data-independent consistency-based motif assessment and ranking (CB-MAR), which is based on the idea that ‘correct motifs’ are more similar to each other while incorrect motifs will differ from each other; and a scoring and classification-based algorithms, which rank binding models by their ability to discriminate sequences known to contain binding sites from those without. The CB-MAR and scoring techniques have a 0.86 and 0.73 median rank correlation using ChIP-seq and PBM respectively. Best motifs selected by CB-MAR achieve a mean AUC of 0.75, comparable to those ranked by held out data at 0.76 – this is based on ChIP-seq motif discovery using five algorithms on 110 transcription factors. We have demonstrated the benefit of this web server in motif choice and ranking, as well as in motif discovery. It can be accessed at http://www.bioinf.ict.ru.ac.za/ .