Technology Report ARTICLE
BAC-BROWSER: the tool for visualization and analysis of prokaryotic genomes
- 1Federal Research and Clinical Center, Federal Medical-Biological Agency, Russia
- 2Institute of Bioorganic Chemistry (RAS), Russia
- 3Moscow Institute of Physics and Technology, Russia
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 usage
BAC-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.
Keywords: genome browser, visualization, Genome, Genes, Viewer, Bacteria, prokaryotes
Received: 09 Aug 2018;
Accepted: 05 Nov 2018.
Edited by:Andrea Masotti, Bambino Gesù Ospedale Pediatrico (IRCCS), Italy
Reviewed by:Sotirios Vasileiadis, University of Thessaly, Greece
Antonella Celluzzi, Bambino Gesù Ospedale Pediatrico (IRCCS), Italy
Copyright: © 2018 Garanina, Fisunov and Govorun. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
* Correspondence: Dr. Gleb Y. Fisunov, Federal Research and Clinical Center, Federal Medical-Biological Agency, Moscow, 115682, Moscow Oblast, Russia, email@example.com