{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2024,5,8]],"date-time":"2024-05-08T06:35:35Z","timestamp":1715150135130},"reference-count":10,"publisher":"Oxford University Press (OUP)","issue":"17","license":[{"start":{"date-parts":[[2021,2,1]],"date-time":"2021-02-01T00:00:00Z","timestamp":1612137600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/open_access\/funder_policies\/chorus\/standard_publication_model"}],"funder":[{"name":"ELIXIR CZ Research Infrastructure Project [MEYS","award":["LM2015047"],"award-info":[{"award-number":["LM2015047"]}]},{"name":"European Regional Development Fund\u2014Project \u2018ELIXIR-CZ: Budov\u00e1n\u00ed kapacit\u2019","award":["CZ.02.1.01\/0.0\/0.0\/16_013\/0001777"],"award-info":[{"award-number":["CZ.02.1.01\/0.0\/0.0\/16_013\/0001777"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2021,9,9]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Summary<\/jats:title>\n                  <jats:p>We present a web service for improving characterization of non-coding RNAs (ncRNAs) from NCBI BLAST outputs, based on a command-line application rboAnalyzer. Briefly, the application extends subject sequences of selected high scoring pairs (HSPs) in BLAST output to their plausible full length, and predicts their homology and secondary structures. The aim of the application is to aid to characterize subject RNAs in HSPs that come uncharacterized in BLAST output. The main advantages of the web-server are easy use and interactive analysis with search, filtering and data export options.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>The web server is freely available at rboanalyzer.elixir-czech.cz. The website frontend is implemented in Elm, while backend is implemented in Python and served by Apache.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btab073","type":"journal-article","created":{"date-parts":[[2021,1,27]],"date-time":"2021-01-27T20:11:14Z","timestamp":1611778274000},"page":"2755-2756","source":"Crossref","is-referenced-by-count":1,"title":["rboAnalyzer webserver: web service for non-coding RNA characterization from NCBI BLAST output"],"prefix":"10.1093","volume":"37","author":[{"given":"Marek","family":"Schwarz","sequence":"first","affiliation":[{"name":"Laboratory of Bioinformatics, Institute of Microbiology, The Czech Academy of Sciences , Praha, Czech Republic"}]},{"given":"Ji\u0159\u00ed","family":"Vohradsk\u00fd","sequence":"additional","affiliation":[{"name":"Laboratory of Bioinformatics, Institute of Microbiology, The Czech Academy of Sciences , Praha, Czech Republic"}]},{"given":"Josef","family":"P\u00e1nek","sequence":"additional","affiliation":[{"name":"Laboratory of Bioinformatics, Institute of Microbiology, The Czech Academy of Sciences , Praha, Czech Republic"}]}],"member":"286","published-online":{"date-parts":[[2021,2,1]]},"reference":[{"key":"2023051609213554100_btab073-B1","doi-asserted-by":"crossref","first-page":"D36","DOI":"10.1093\/nar\/gks1195","article-title":"GenBank","volume":"41","author":"Benson","year":"2012","journal-title":"Nucleic Acids Res"},{"key":"2023051609213554100_btab073-B2","doi-asserted-by":"crossref","first-page":"421.","DOI":"10.1186\/1471-2105-10-421","article-title":"BLAST plus: architecture and applications","volume":"10","author":"Camacho","year":"2009","journal-title":"BMC Bioinformatics"},{"key":"2023051609213554100_btab073-B3","doi-asserted-by":"crossref","first-page":"1974","DOI":"10.1093\/bioinformatics\/btp250","article-title":"VARNA: interactive drawing and editing of the RNA secondary structure","volume":"25","author":"Darty","year":"2009","journal-title":"Bioinformatics"},{"key":"2023051609213554100_btab073-B4","doi-asserted-by":"crossref","first-page":"D335","DOI":"10.1093\/nar\/gkx1038","article-title":"Rfam 13.0: shifting to a genome-centric resource for non-coding RNA families","volume":"46","author":"Kalvari","year":"2018","journal-title":"Nucleic Acids Res"},{"key":"2023051609213554100_btab073-B5","doi-asserted-by":"crossref","first-page":"44.","DOI":"10.1186\/1471-2105-4-44","article-title":"RSEARCH: finding homologs of single structured RNA sequences","volume":"4","author":"Klein","year":"2003","journal-title":"BMC Bioinformatics"},{"key":"2023051609213554100_btab073-B6","author":"Robinson","year":"2020"},{"key":"2023051609213554100_btab073-B7","doi-asserted-by":"crossref","first-page":"675","DOI":"10.3389\/fgene.2020.00675","article-title":"rboAnalyzer: a software to improve characterization of non-coding RNAs from sequence database search output","volume":"11","author":"Schwarz","year":"2020","journal-title":"Front. 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