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HTS-IBIS: fast and accurate inference of binding site motifs from HT-SELEX data

By Yaron Orenstein, Ron Shamir

Posted 08 Jul 2015
bioRxiv DOI: 10.1101/022277

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.

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