Разработка программного комплекса WebMCOT для поиска совместно встречаемых ДНК-мотивов сайтов связывания транскрипционных факторов

Abstract

Regulation of eukaryotic gene transcription is controlled by specific proteins transcription factors. Transcription factors bind certain regions of genomic DNA (binding sites or motives). Common action of two or more transcription factors is widespread mechanism of transcription factor action. Hence, the term ‘composite element’ implied two closely located and frequently occurred in genomic DNA motives. Composite elements are partitioned onto those with two overlapped motifs, or with these two motifs separated with a spacer. Currently, the chromatin immunoprecipitation high throughput approach ChIP-seq is used to locate binding sites for a certain “anchor” transcription factor in vivo in genomic scale. Thus, the search of composite elements with the help of ChIP-seq whole-genome transcription factor binding profiles is the actual bioinformatics issue. But existing approaches for prediction of composite elements on the basis of ChIP-seq data either omit an overlap of motifs (but require only a single ChIP-seq dataset) or consider an overlap of motifs (but require additional ChIP-seq data for a partner motif). But, ChIP-seq experiments are very expensive. In the Institute of Cytology and Genetics, MCOT program has been recently developed. It performs search of motifs taking into account their overlaps based on a single ChIP-seq dataset. MCOT is a console application and does not have many user friendly functions like data preparation and report generation. This work presents a web service WebMCOT for prediction of co-occurred DNA motifs in ChIP-seq data. WebMCOT consists of three parts: client, server, and worker. Software tools list, architecture and web interface are presented.