Riboswitch Scanner statistics

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Riboswitch Scanner specifications

Information


Unique identifier OMICS_10443
Name Riboswitch Scanner
Interface Web user interface
Restrictions to use None
Input data DNA sequence
Input format FASTA
Computer skills Basic
Stability Stable
Maintained Yes

Maintainer


  • person_outline Supratim Sengupta

Publications for Riboswitch Scanner

Riboswitch Scanner citations

 (4)
library_books

Phylogenomic and comparative analysis of the distribution and regulatory patterns of TPP riboswitches in fungi

2018
Sci Rep
PMCID: 5882874
PMID: 29615754
DOI: 10.1038/s41598-018-23900-7

[…] The gene-specific TPP riboswitches detected by the Riboswitch Scanner were mapped onto well-resolved phylogenetic trees to present the distribution of these riboswitches across all fully sequenced fungal genomes. We analyzed this distribution and clas […]

library_books

Using RNA Sequence and Structure for the Prediction of Riboswitch Aptamer: A Comprehensive Review of Available Software and Tools

2018
Front Genet
PMCID: 5780412
PMID: 29403526
DOI: 10.3389/fgene.2017.00231

[…] Riboswitch Scanner (Mukherjee and Sengupta, ) is a web server capable of detecting 24 riboswitch classes and identifying novel riboswitches. Its algorithm utilizes 5-fold cross-validated HMM models cr […]

library_books

Comparative genomics and phylogenomic analyses of lysine riboswitch distributions in bacteria

2017
PLoS One
PMCID: 5584792
PMID: 28873470
DOI: 10.1371/journal.pone.0184314

[…] l of sequence conservation of the aptamer domain in each class of riboswitch, we had developed a pHMM-based model for fast and accurate detection of riboswitches []. Recently, a web-server called the Riboswitch Scanner [] was developed to provide researchers with a user-friendly tool for detecting riboswitches and even T-box RNA’s with high sensitivity and specificity from both partial and complet […]

library_books

Genomic Analysis of a New Serovar of Leptospira weilii Serogroup Manhao

2017
Front Microbiol
PMCID: 5288384
PMID: 28210253
DOI: 10.3389/fmicb.2017.00149

[…] is associated with distinct metabolic capacities amongst Leptospira spp. (; ). To further analyze other non-coding RNA elements in the strain L231 genome, riboswitch predictions were performed using Riboswitch Scanner (). In agreement with the previous studies (; ), three riboswitches associated with transport and vitamin biosynthesis were found. Of these, two elements are located upstream of L23 […]

Citations

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Riboswitch Scanner institution(s)
Department of Physical Sciences, Indian Institute of Science Education and Research Kolkata, Mohanpur, India
Riboswitch Scanner funding source(s)
The work was partially funded by a Centre of Excellence (COE) grant provided by the Dept. of Biotechnology, Govt. of India to the Centre for Computational Biology and Bioinformatics (CCBB) and by a UGC-ISF grant awarded under the India-Israel joint research project.

Riboswitch Scanner reviews

 (2)
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Anonymous user #3368's avatar image No country

Anonymous user #3368

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Web
Important webtool for riboswitch prediction from bacterial complete genome sequence. Prediction rates are very high. For searching one class of riboswitch in a complete bacterial genome sequence the webtool takes 3 min to generate the output and for searching multiple classes at a time, the webtool takes several min to generate the complete output.
Anonymous user #3367's avatar image No country

Anonymous user #3367

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Web
Very efficient webserver for detecting riboswitches from complete genomic sequence.