{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,2,23]],"date-time":"2025-02-23T21:40:26Z","timestamp":1740346826318,"version":"3.37.3"},"reference-count":25,"publisher":"Oxford University Press (OUP)","issue":"2","license":[{"start":{"date-parts":[[2024,5,10]],"date-time":"2024-05-10T00:00:00Z","timestamp":1715299200000},"content-version":"vor","delay-in-days":5092,"URL":"https:\/\/creativecommons.org\/licenses\/by-nc-sa\/3.0\/"}],"funder":[{"name":"Bioinformatics Centre"},{"name":"Supercomputer Education and Research Centre"},{"name":"Indian Institute of Science and the Interactive Graphics Facility"},{"DOI":"10.13039\/100007780","name":"Indian Institute of Science","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100007780","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Department of Biotechnology"},{"name":"Government of India"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2010,6,1]]},"abstract":"<jats:title>Abstract<\/jats:title><jats:p>Small RNAs (sRNAs) are non-coding transcripts exerting their functions in the cells directly. Identification of sRNAs is a difficult task due to the lack of clear sequence and structural biases. Most sRNAs are identified within genus specific intergenic regions in related genomes. However, several of these regions remain un-annotated due to lack of sequence homology and\/or potent statistical identification tools. A computational engine has been built to search within the intergenic regions to identify and roughly annotate new putative sRNA regions in Enterobacteriaceae genomes. It utilizes experimentally known sRNA data and their flanking genes\/KEGG Orthology (KO) numbers as templates to identify similar sRNA regions in related query genomes. The search engine not only has the capability to locate putative intergenic regions for specific sRNAs, but also has the potency to locate conserved, shuffled or deleted gene clusters in query genomes. Because it uses the KO terms for locating functionally important regions such as sRNAs, any further KO number assignment to additional genes will increase the sensitivity. The PsRNA server is used for the identification of putative sRNA regions through the information retrieved from the sRNA of interest. The computing engine is available online at http:\/\/bioserver1.physics.iisc.ernet.in\/psrna\/ and http:\/\/bicmku.in:8081\/psrna\/.<\/jats:p>","DOI":"10.1016\/s1672-0229(10)60014-9","type":"journal-article","created":{"date-parts":[[2010,8,5]],"date-time":"2010-08-05T09:10:46Z","timestamp":1280999446000},"page":"127-134","source":"Crossref","is-referenced-by-count":6,"title":["PsRNA: A Computing Engine for the Comparative Identification of Putative Small RNA Locations within Intergenic Regions"],"prefix":"10.1093","volume":"8","author":[{"given":"Jayavel","family":"Sridhar","sequence":"first","affiliation":[{"name":"Centre of Excellence in Bioinformatics, School of Biotechnology, Madurai Kamaraj University , Madurai, 625021 , India"}]},{"given":"Govindaraj","family":"Sowmiya","sequence":"additional","affiliation":[{"name":"Bioinformatics Centre, Indian Institute of Science , Bangalore, 560012 , India"}]},{"given":"Kanagaraj","family":"Sekar","sequence":"additional","affiliation":[{"name":"Bioinformatics Centre, Indian Institute of Science , Bangalore, 560012 , India"},{"name":"Supercomputer Education and Research Centre, Indian Institute of Science , Bangalore, 560012 , India"}]},{"given":"Ziauddin Ahamed","family":"Rafi","sequence":"additional","affiliation":[{"name":"Centre of Excellence in Bioinformatics, School of Biotechnology, Madurai Kamaraj University , Madurai, 625021 , India"}]}],"member":"286","published-online":{"date-parts":[[2010,8,4]]},"reference":[{"key":"2024051008272959200_bib1","doi-asserted-by":"crossref","first-page":"1260","DOI":"10.1126\/science.1072249","article-title":"An expanding universe of noncoding RNA","volume":"296","author":"Storz","year":"2002","journal-title":"Science"},{"key":"2024051008272959200_bib2","doi-asserted-by":"crossref","first-page":"R17","DOI":"10.1093\/hmg\/ddl046","article-title":"Non-coding RNA","volume":"15","author":"Mattick","year":"2006","journal-title":"Hum. Mol. Genet."},{"key":"2024051008272959200_bib3","doi-asserted-by":"crossref","first-page":"1637","DOI":"10.1101\/gad.901001","article-title":"Identification of novel small RNAs using comparative genomics and microarrays","volume":"15","author":"Wassarman","year":"2001","journal-title":"Genes Dev."},{"key":"2024051008272959200_bib4","doi-asserted-by":"crossref","first-page":"262","DOI":"10.1016\/j.mib.2007.06.001","article-title":"Target identification of small noncoding RNAs in bacteria","volume":"10","author":"Vogel","year":"2007","journal-title":"Curr. Opin. Microbiol."},{"key":"2024051008272959200_bib5","doi-asserted-by":"crossref","first-page":"156","DOI":"10.1016\/j.mib.2007.03.007","article-title":"CsrB sRNA family: sequestration of RNA-binding regulatory proteins","volume":"10","author":"Babitzke","year":"2007","journal-title":"Curr. Opin. Microbiol."},{"key":"2024051008272959200_bib6","doi-asserted-by":"crossref","first-page":"137","DOI":"10.1016\/S0092-8674(02)00727-4","article-title":"Computational genomics of noncoding RNA genes","volume":"139","author":"Eddy","year":"2002","journal-title":"Cell"},{"key":"2024051008272959200_bib7","doi-asserted-by":"crossref","first-page":"439","DOI":"10.1093\/nar\/gkg006","article-title":"Rfam: an RNA family database","volume":"31","author":"Griffiths-Jones","year":"2003","journal-title":"Nucleic Acids Res."},{"key":"2024051008272959200_bib8","doi-asserted-by":"crossref","first-page":"D112","DOI":"10.1093\/nar\/gki041","article-title":"NONCODE: an integrated knowledge database of non-coding RNAs","volume":"33","author":"Liu","year":"2005","journal-title":"Nucleic Acids Res."},{"key":"2024051008272959200_bib9","doi-asserted-by":"crossref","first-page":"D277","DOI":"10.1093\/nar\/gkh063","article-title":"The KEGG resource for deciphering the genome","volume":"32","author":"Kanehisa","year":"2004","journal-title":"Nucleic Acids Res."},{"key":"2024051008272959200_bib10","doi-asserted-by":"crossref","first-page":"D34","DOI":"10.1093\/nar\/gki063","article-title":"GenBank","volume":"33","author":"Benson","year":"2005","journal-title":"Nucleic Acids Res."},{"key":"2024051008272959200_bib11","doi-asserted-by":"crossref","first-page":"74","DOI":"10.1089\/omi.2006.0006","article-title":"Small RNA identification in Enterobacteriaceae using synteny and genomic backbone retention","volume":"11","author":"Sridhar","year":"2007","journal-title":"OMICS"},{"key":"2024051008272959200_bib12","doi-asserted-by":"crossref","first-page":"601","DOI":"10.3233\/ISI-2007-00333","article-title":"Identification of novel genomic islands associated with small RNAs","volume":"7","author":"Sridhar","year":"2007","journal-title":"In Silico Biol."},{"key":"2024051008272959200_bib13","doi-asserted-by":"crossref","first-page":"284","DOI":"10.6026\/97320630002284","article-title":"Functional annotations in bacterial genomes based on small RNA signatures","volume":"2","author":"Sridhar","year":"2008","journal-title":"Bioinformation"},{"key":"2024051008272959200_bib14","doi-asserted-by":"crossref","first-page":"1544","DOI":"10.1093\/nar\/gki296","article-title":"Integration of text- and data-mining using ontologies successfully selects disease gene candidates","volume":"33","author":"Tiffin","year":"2005","journal-title":"Nucleic Acids Res."},{"key":"2024051008272959200_bib15","doi-asserted-by":"crossref","first-page":"3787","DOI":"10.1093\/bioinformatics\/bti430","article-title":"Automated genome annotation and pathway identification using the KEGG Orthology (KO) as a controlled vocabulary","volume":"21","author":"Mao","year":"2005","journal-title":"Bioinformatics"},{"key":"2024051008272959200_bib16","doi-asserted-by":"crossref","first-page":"3160","DOI":"10.1073\/pnas.0308653100","article-title":"Trends between gene content and genome size in prokaryotic species with larger genomes","volume":"101","author":"Konstantinidis","year":"2004","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"2024051008272959200_bib17","first-page":"342","article-title":"Identification of ortholog groups in KEGG\/SSDB by considering domain structures","volume":"13","author":"Itoh","year":"2002","journal-title":"Genome Informatics"},{"key":"2024051008272959200_bib18","doi-asserted-by":"crossref","first-page":"8","DOI":"10.1186\/1471-2105-2-8","article-title":"Noncoding RNA gene detection using comparative sequence analysis","volume":"2","author":"Rivas","year":"2001","journal-title":"BMC Bioinformatics"},{"key":"2024051008272959200_bib19","doi-asserted-by":"crossref","first-page":"2454","DOI":"10.1073\/pnas.0409169102","article-title":"Fast and reliable prediction of noncoding RNAs","volume":"102","author":"Washietl","year":"2005","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"2024051008272959200_bib20","doi-asserted-by":"crossref","first-page":"D121","DOI":"10.1093\/nar\/gki081","article-title":"Rfam: annotating non-coding RNAs in complete genomes","volume":"33","author":"Griffiths-Jones","year":"2005","journal-title":"Nucleic Acids Res."},{"key":"2024051008272959200_bib21","doi-asserted-by":"crossref","first-page":"1813","DOI":"10.1093\/nar\/gkg297","article-title":"A survey of small RNA-encoding genes in Escherichia coli","volume":"31","author":"Hershberg","year":"2003","journal-title":"Nucleic Acids Res."},{"key":"2024051008272959200_bib22","doi-asserted-by":"crossref","first-page":"1453","DOI":"10.1126\/science.277.5331.1453","article-title":"The complete genome sequence of Escherichia coli K-12","volume":"277","author":"Blattner","year":"1997","journal-title":"Science"},{"key":"2024051008272959200_bib23","doi-asserted-by":"crossref","first-page":"1211","DOI":"10.1128\/jb.152.3.1211-1219.1982","article-title":"Identification of two genes immediately downstream from the polA gene of Escherichia coli","volume":"152","author":"Joyce","year":"1982","journal-title":"J. Bacteriol."},{"key":"2024051008272959200_bib24","doi-asserted-by":"crossref","first-page":"12879","DOI":"10.1073\/pnas.0603038103","article-title":"How to become a uropathogen: comparative genomic anlaysis of extraintestinal pathogenic Escherichia coli strains","volume":"103","author":"Brzuszkiewicz","year":"2006","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"2024051008272959200_bib25","doi-asserted-by":"crossref","first-page":"261","DOI":"10.1089\/omi.2008.0067","article-title":"Small RNA identification in Enterobacteriaceae using synteny and genomic backbone retention II","volume":"13","author":"Sridhar","year":"2009","journal-title":"OMICS"}],"container-title":["Genomics, Proteomics &amp; Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/api.elsevier.com\/content\/article\/PII:S1672022910600149?httpAccept=text\/xml","content-type":"text\/xml","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/api.elsevier.com\/content\/article\/PII:S1672022910600149?httpAccept=text\/plain","content-type":"text\/plain","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/academic.oup.com\/gpb\/article-pdf\/8\/2\/127\/57483137\/gpb_8_2_127.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/gpb\/article-pdf\/8\/2\/127\/57483137\/gpb_8_2_127.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,2,23]],"date-time":"2025-02-23T21:23:09Z","timestamp":1740345789000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/gpb\/article\/8\/2\/127\/7221853"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2010,6,1]]},"references-count":25,"journal-issue":{"issue":"2","published-print":{"date-parts":[[2010,6,1]]}},"URL":"https:\/\/doi.org\/10.1016\/s1672-0229(10)60014-9","relation":{},"ISSN":["1672-0229","2210-3244"],"issn-type":[{"type":"print","value":"1672-0229"},{"type":"electronic","value":"2210-3244"}],"subject":[],"published-other":{"date-parts":[[2010,6]]},"published":{"date-parts":[[2010,6,1]]}}}