Deep and wide digging for binding motifs in ChIP-Seq data
2010; Oxford University Press; Volume: 26; Issue: 20 Linguagem: Inglês
10.1093/bioinformatics/btq488
ISSN1367-4811
AutoresIvan V. Kulakovskiy, Valentina Boeva, Alexander V. Favorov, Vsevolod J. Makeev,
Tópico(s)RNA and protein synthesis mechanisms
ResumoChIP-Seq data are a new challenge for motif discovery. Such a data typically consists of thousands of DNA segments with base-specific coverage values. We present a new version of our DNA motif discovery software ChIPMunk adapted for ChIP-Seq data. ChIPMunk is an iterative algorithm that combines greedy optimization with bootstrapping and uses coverage profiles as motif positional preferences. ChIPMunk does not require truncation of long DNA segments and it is practical for processing up to tens of thousands of data sequences. Comparison with traditional (MEME) or ChIP-Seq-oriented (HMS) motif discovery tools shows that ChIPMunk identifies the correct motifs with the same or better quality but works dramatically faster.ChIPMunk is freely available within the ru_genetika Java package: http://line.imb.ac.ru/ChIPMunk. Web-based version is also available.ivan.kulakovskiy@gmail.comSupplementary data are available at Bioinformatics online.
Referência(s)