RiboD: A comprehensive database for prokaryotic riboswitches

Sumit Mukherjee; Sukhen Das Mandal; Nikita Gupta; Matan Drory-Retwitzer; Danny Barash; Supratim Sengupta

doi:https://doi.org/10.1093/bioinformatics/btz093

RiboD: A comprehensive database for prokaryotic riboswitches

Sumit Mukherjee, Sukhen Das Mandal, Nikita Gupta, Matan Drory-Retwitzer, Danny Barash, Supratim Sengupta

Department of Computer Science

Ben-Gurion University of the Negev

Research output: Contribution to journal › Article › peer-review

Abstract

Riboswitches are cis-regulatory non-coding genomic segments that control the expression of downstream genes by undergoing conformational change upon ligand binding. We present a comprehensive database of prokaryotic riboswitches that allows the user to search for riboswitches using multiple criteria, extract information about riboswitch location and gene/operon it regulates. RiboD provides a very useful resource that can be utilized for the better understanding of riboswitch-based gene regulation in bacteria and archaea. Availability and implementation: RiboD can be freely accessed on the web at http://ribod.iiserkol.ac.in/.

Original language	American English
Pages (from-to)	3541-3543
Number of pages	3
Journal	Bioinformatics
Volume	35
Issue number	18
DOIs	https://doi.org/10.1093/bioinformatics/btz093
State	Published - 15 Sep 2019

All Science Journal Classification (ASJC) codes

Computational Mathematics
Molecular Biology
Biochemistry
Statistics and Probability
Computer Science Applications
Computational Theory and Mathematics

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https://doi.org/10.1093/bioinformatics/btz093

Cite this

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title = "RiboD: A comprehensive database for prokaryotic riboswitches",

abstract = "Riboswitches are cis-regulatory non-coding genomic segments that control the expression of downstream genes by undergoing conformational change upon ligand binding. We present a comprehensive database of prokaryotic riboswitches that allows the user to search for riboswitches using multiple criteria, extract information about riboswitch location and gene/operon it regulates. RiboD provides a very useful resource that can be utilized for the better understanding of riboswitch-based gene regulation in bacteria and archaea. Availability and implementation: RiboD can be freely accessed on the web at http://ribod.iiserkol.ac.in/.",

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AU - Drory-Retwitzer, Matan

AU - Barash, Danny

AU - Sengupta, Supratim

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AB - Riboswitches are cis-regulatory non-coding genomic segments that control the expression of downstream genes by undergoing conformational change upon ligand binding. We present a comprehensive database of prokaryotic riboswitches that allows the user to search for riboswitches using multiple criteria, extract information about riboswitch location and gene/operon it regulates. RiboD provides a very useful resource that can be utilized for the better understanding of riboswitch-based gene regulation in bacteria and archaea. Availability and implementation: RiboD can be freely accessed on the web at http://ribod.iiserkol.ac.in/.

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RiboD: A comprehensive database for prokaryotic riboswitches

Abstract

All Science Journal Classification (ASJC) codes

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