PT  - JOURNAL ARTICLE
AU  - Yaron Orenstein
AU  - Ron Shamir
TI  - HTS-IBIS: fast and accurate inference of binding site motifs from HT-SELEX data
AID  - 10.1101/022277
DP  - 2015 Jan 01
TA  - bioRxiv
PG  - 022277
4099  - http://biorxiv.org/content/early/2015/07/08/022277.short
4100  - http://biorxiv.org/content/early/2015/07/08/022277.full
AB  - Summary Recent technological advancements enable measuring the binding of a transcription factor to thousands of DNA sequences, in order to infer its binding preferences. High-throughput-SELEX measures protein-DNA binding by deep sequencing over several cycles of enrichment. We devised a new algorithm called HTS-IBIS for the inference task. HTS-IBIS corrects for technological biases, selects the cycle and k, and builds a motif starting from a consensus k-mer in that cycle. In large scale tests, HTS-IBIS outperformed the extant automatic algorithm for the motif finding task on both in vitro and in vivo binding prediction.Availability HTS-IBIS is available on acgt.cs.tau.ac.il/HTS-IBIS.Contact rshamir{at}tau.ac.il