{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,4,9]],"date-time":"2025-04-09T06:06:13Z","timestamp":1744178773801},"reference-count":7,"publisher":"Oxford University Press (OUP)","issue":"15","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2011,8,1]]},"abstract":"Abstract<\/jats:title>\n Motivation: Structural alignment of RNA is found to be a useful computational technique for idenitfying non-coding RNAs (ncRNAs). However, existing tools do not handle structures with pseudoknots. Although algorithms exist that can handle structural alignment for different types of pseudoknots, no software tools are available and users have to determine the type of pseudoknots to select the appropriate algoirthm to use which limits the usage of structural alignment in identifying novel ncRNAs.<\/jats:p>\n Results: We implemented the first web server, RNASAlign, which can automatically identify the pseudoknot type of a secondary structure and perform structural alignment of a folded RNA with every region of a target DNA\/RNA sequence. Regions with high similarity scores and low e-values, together with the detailed alignments will be reported to the user. Experiments on more than 350 ncRNA families show that RNASAlign is effective.<\/jats:p>\n Availability: \u00a0http:\/\/www.bio8.cs.hku.hk\/RNASAlign.<\/jats:p>\n Contact: \u00a0smyiu@cs.hku.hk<\/jats:p>","DOI":"10.1093\/bioinformatics\/btr338","type":"journal-article","created":{"date-parts":[[2011,6,10]],"date-time":"2011-06-10T08:13:35Z","timestamp":1307693615000},"page":"2151-2152","source":"Crossref","is-referenced-by-count":5,"title":["RNASAlign: RNA Structural Alignment System"],"prefix":"10.1093","volume":"27","author":[{"given":"Thomas K. F.","family":"Wong","sequence":"first","affiliation":[{"name":"1 Department of Computer Science, The University of Hong Kong, Pokfulam Road, Hong Kong and 2Department of Computer Science, National Tsing Hua University, Taiwan"}]},{"given":"Kwok-Lung","family":"Wan","sequence":"additional","affiliation":[{"name":"1 Department of Computer Science, The University of Hong Kong, Pokfulam Road, Hong Kong and 2Department of Computer Science, National Tsing Hua University, Taiwan"}]},{"given":"Bay-Yuan","family":"Hsu","sequence":"additional","affiliation":[{"name":"1 Department of Computer Science, The University of Hong Kong, Pokfulam Road, Hong Kong and 2Department of Computer Science, National Tsing Hua University, Taiwan"}]},{"given":"Brenda W. Y.","family":"Cheung","sequence":"additional","affiliation":[{"name":"1 Department of Computer Science, The University of Hong Kong, Pokfulam Road, Hong Kong and 2Department of Computer Science, National Tsing Hua University, Taiwan"}]},{"given":"Wing-Kai","family":"Hon","sequence":"additional","affiliation":[{"name":"1 Department of Computer Science, The University of Hong Kong, Pokfulam Road, Hong Kong and 2Department of Computer Science, National Tsing Hua University, Taiwan"}]},{"given":"Tak-Wah","family":"Lam","sequence":"additional","affiliation":[{"name":"1 Department of Computer Science, The University of Hong Kong, Pokfulam Road, Hong Kong and 2Department of Computer Science, National Tsing Hua University, Taiwan"}]},{"given":"Siu-Ming","family":"Yiu","sequence":"additional","affiliation":[{"name":"1 Department of Computer Science, The University of Hong Kong, Pokfulam Road, Hong Kong and 2Department of Computer Science, National Tsing Hua University, Taiwan"}]}],"member":"286","published-online":{"date-parts":[[2011,6,8]]},"reference":[{"key":"2023012511531571800_B1","doi-asserted-by":"crossref","first-page":"45","DOI":"10.1038\/nature02642","article-title":"Crystal structure of a self-splicing group I intron with both exons","volume":"430","author":"Adams","year":"2004","journal-title":"Nature"},{"key":"2023012511531571800_B2","doi-asserted-by":"crossref","first-page":"11665","DOI":"10.1021\/bi00162a001","article-title":"Structural and functional aspects of RNA pseudoknots","volume":"31","author":"Dam","year":"1992","journal-title":"Biochemistry"},{"key":"2023012511531571800_B3","doi-asserted-by":"crossref","first-page":"489","DOI":"10.1089\/cmb.2007.0214","article-title":"Structural alignment of pseudoknotted RNA","volume":"15","author":"Han","year":"2008","journal-title":"J. Comput. Biol."},{"key":"2023012511531571800_B4","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":"2023012511531571800_B5","article-title":"A Memory Efficient Algorithm for Structural Alignment of RNAs with Pseudoknots","volume-title":"IEEE\/ACM TCBB","author":"Wong","year":"2011"},{"key":"2023012511531571800_B6","doi-asserted-by":"crossref","first-page":"97","DOI":"10.1089\/cmb.2009.0275","article-title":"Structural alignment of RNA with complex pseudoknot structure","volume":"18","author":"Wong","year":"2011","journal-title":"J. Comput. Biol."},{"key":"2023012511531571800_B7","first-page":"4","article-title":"Searching genomes for noncoding RNA using FastR","volume":"2","author":"Zhang","year":"2005","journal-title":"IEEE\/ACM TCBB"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/27\/15\/2151\/48864781\/bioinformatics_27_15_2151.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/27\/15\/2151\/48864781\/bioinformatics_27_15_2151.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,1,25]],"date-time":"2023-01-25T11:58:30Z","timestamp":1674647910000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/27\/15\/2151\/402983"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2011,6,8]]},"references-count":7,"journal-issue":{"issue":"15","published-print":{"date-parts":[[2011,8,1]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btr338","relation":{},"ISSN":["1367-4811","1367-4803"],"issn-type":[{"value":"1367-4811","type":"electronic"},{"value":"1367-4803","type":"print"}],"subject":[],"published-other":{"date-parts":[[2011,8,1]]},"published":{"date-parts":[[2011,6,8]]}}}