RT Journal Article
SR Electronic
T1 HTS-IBIS: fast and accurate inference of binding site motifs from HT-SELEX data
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 022277
DO 10.1101/022277
A1 Yaron Orenstein
A1 Ron Shamir
YR 2015
UL http://biorxiv.org/content/early/2015/07/08/022277.abstract
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