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Increasing volumes of genomic data on the location of binding sites for transcription factors, chromosomal contacts, annotation of genomic characteristics obtained with the help of modern sequencing technologies require the development of new software for their analysis, optimization of existing processing algorithms. Supercomputer calculations allow solving the tasks of studying the regulation of gene transcription at a qualitatively new level. The problems of analysis of genomic sequencing data obtained on the basis of ChIP-seq, ChIA-PET and Hi-C technologies are considered. Presented are computer approaches and programs developed by the authors to solve the proposed problems of genomics, a discussion is given on further directions of development.