Abstract
Prokaryotes are actively studied objects in the scope of genomic regulation. Microbiologists need special tools for complex analysis of data to study and identification of regulatory mechanism in bacteria and archaea.We developed a tool BAC-BROWSER, specifically for visualization and analysis of small prokaryotic genomes. BAC-BROWSER provides tools for different types of analysis to study a wide set of regulatory mechanisms of prokaryotes: -transcriptional regulation by transcription factors (TFs), analysis of TFs, their targets, and binding sites.-other regulatory motifs, promoters, terminators and ribosome binding sites-transcriptional regulation by variation of operon structure, alternative starts or ends of transcription.-non-coding RNAs, antisense RNAs-RNA secondary structure, riboswitches-GC content, GC skew, codon usageBAC-browser incorporated free programs accelerating the verification of obtained results: primer design and oligocalculator, vector visualization, the tool for synthetic gene construction. The program is designed for Windows operating system and freely available for download in http://smdb.rcpcm.org/tools/index.html.
Highlights
Prokaryotes are the great source for discovery of new regulatory mechanisms
We developed new genome browser BAC-BROWSER designed for molecular biologists and microbiologists that combine user-friendly interface with multiple functions for prokaryotic regulation analysis
Based on BACBROWSER prediction we identified TSSs and gene promoters that helped to reveal a new mechanism of transcriptional regulation and reconstruct transcriptional control network for three bacteria species (Mazin et al, 2014; Fisunov et al, 2016)
Summary
Prokaryotes are the great source for discovery of new regulatory mechanisms. Their diversity and relative simplicity of genome organization make them suitable objects for different -omics and comparative analysis. We developed new genome browser BAC-BROWSER designed for molecular biologists and microbiologists that combine user-friendly interface with multiple functions for prokaryotic regulation analysis. Using RNA-seq read coverage BAC-BROWSER can identify TSSs and terminators, map and visualize TUs. BAC-BROWSER provides a wide set of algorithms for analysis of genes, proteins, regulatory motifs and structural elements, like hairpins and riboswitches.
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