Motif Discovery and Motif Finding in ChIP-Seq Data
Ivan V. Kulakovskiy and Vsevolod J. Makeev
from: Genome Analysis: Current Procedures and Applications (Edited by: Maria S. Poptsova). Caister Academic Press, U.K. (2014)
Modern bioinformatics and molecular biology research are impossible to imagine without application of high-throughput DNA sequencing technologies, also called next-generation sequencing technologies. In particular, transcriptional regulation studies determining how different genes become "on" and "off" in different tissues in different conditions rely heavily on next-generation sequencing. The ChIP-Seq technology implying chromatin immunoprecipitation followed by deep sequencing allows genome-wide in vivo studies of binding sites for different transcription factors, the proteins that can specifically facilitate or prevent proper construction of the transcription initiatory complex necessary to activate transcription of a specific gene. Transcription initiation control in higher eukaryotes is extremely complex, and its analysis is especially difficult because of the genome size and comparably short transcription factor binding sites. Availability of ChIP-Seq data provided new insights into genome-wide distribution of transcription factor binding sites. It was a new challenge for computational biology to handle enormous amounts of data and detect actual binding sites within DNA segments identified by ChIP-Seq. Here we focus on application and advances of motif discovery and motif finding, a very well-established field in bioinformatics of sequence analysis, which has been given a second birth by the ChIP-Seq technology read more ...