Fast growth of sequencing data volume demands development of new program systems for processing, storage and analysis of sequencing data. Here we review approaches for data bioinformatics integration using complementary approaches in genomics, proteomics and supercomputer calculations on example of ICGenomics tool. The program complex ICGenomics has been designed previously in Novosibirsk for storage, mining, and analysis of genomic sequences. This tool enables wet-lab biologists to perform high-quality processing of sequencing data in the fields of genomics, biomedicine, and biotechnology. Overall, integrated software tools have to include novel methods of the processing of initial high-throughput sequencing data including gene expression data. Examples of the application areas are: ChIP-seq analysis; functional annotation of gene regulatory regions in nucleotide sequences; prediction of nucleosome positioning; and structural and functional annotation of proteins, including prediction of their allergenicity parameters, as well as estimates of evolution changes in protein families. Applications of the ICGenomics to the analysis of genomic sequences in model genomes are shown. We conclude the presentation by on machine learning methods adaptation in bioinformatics. The ICGenomics tool is available at http://www-bionet.sscc.ru/icgenomics/.