{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,29]],"date-time":"2026-03-29T11:19:55Z","timestamp":1774783195553,"version":"3.50.1"},"reference-count":17,"publisher":"Oxford University Press (OUP)","issue":"5","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2016,3,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Summary: Riboswitches are non-coding RNA located in the 5\u2032 untranslated regions where they bind a target metabolite used to specify the riboswitch class and control the expression of associated genes. Accurate identification of riboswitches is the first step towards understanding their regulatory and functional roles in the cell. In this article, we describe a new web application named Riboswitch Scanner which provides an automated pipeline for pHMM-based detection of riboswitches in partial as well as complete genomic sequences rapidly, with high sensitivity and specificity.<\/jats:p>\n               <jats:p>Availability and implementation: Riboswitch Scanner can be freely accessed on the web at http:\/\/service.iiserkol.ac.in\/\u223criboscan\/.<\/jats:p>\n               <jats:p>Contact: \u00a0mukherjee.sumit89@gmail.com<\/jats:p>\n               <jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btv640","type":"journal-article","created":{"date-parts":[[2015,10,31]],"date-time":"2015-10-31T02:38:11Z","timestamp":1446259091000},"page":"776-778","source":"Crossref","is-referenced-by-count":49,"title":["Riboswitch Scanner: an efficient pHMM-based web-server to detect riboswitches in genomic sequences"],"prefix":"10.1093","volume":"32","author":[{"given":"Sumit","family":"Mukherjee","sequence":"first","affiliation":[{"name":"Department of Physical Sciences, Indian Institute of Science Education and Research Kolkata, Mohanpur-741246, West Bengal, India"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Supratim","family":"Sengupta","sequence":"additional","affiliation":[{"name":"Department of Physical Sciences, Indian Institute of Science Education and Research Kolkata, Mohanpur-741246, West Bengal, India"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2015,10,30]]},"reference":[{"key":"2023020110443734000_btv640-B1","doi-asserted-by":"crossref","first-page":"W690","DOI":"10.1093\/nar\/gki445","article-title":"RibEx: a web server for locating riboswitches and other conserved bacterial regulatory elements","volume":"33","author":"Abreu-Goodger","year":"2005","journal-title":"Nucleic Acids Res."},{"key":"2023020110443734000_btv640-B2","doi-asserted-by":"crossref","first-page":"1426","DOI":"10.1261\/rna.1623809","article-title":"Computational identification of riboswitches based on RNA conserved functional sequences and conformations","volume":"15","author":"Chang","year":"2009","journal-title":"RNA"},{"key":"2023020110443734000_btv640-B3","doi-asserted-by":"crossref","first-page":"497","DOI":"10.1038\/nature05769","article-title":"Control of alternative RNA splicing and gene expression by eukaryotic riboswitches","volume":"447","author":"Cheah","year":"2007","journal-title":"Nature"},{"key":"2023020110443734000_btv640-B4","doi-asserted-by":"crossref","first-page":"755","DOI":"10.1093\/bioinformatics\/14.9.755","article-title":"Profile hidden Markov models","volume":"14","author":"Eddy","year":"1998","journal-title":"Bioinformatics"},{"key":"2023020110443734000_btv640-B5","doi-asserted-by":"crossref","first-page":"e1002195","DOI":"10.1371\/journal.pcbi.1002195","article-title":"Accelerated profile HMM searches","volume":"7","author":"Eddy","year":"2011","journal-title":"PLoS Comput. 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