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Article: RNASAlign: RNA structural alignment system

TitleRNASAlign: RNA structural alignment system
Authors
Issue Date2011
PublisherOxford University Press. The Journal's web site is located at http://bioinformatics.oxfordjournals.org/
Citation
Bioinformatics, 2011, v. 27 n. 15, p. 2151-2152 How to Cite?
AbstractMotivation: 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. 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. © The Author 2011. Published by Oxford University Press. All rights reserved.
Persistent Identifierhttp://hdl.handle.net/10722/140790
ISSN
2015 Impact Factor: 5.766
2015 SCImago Journal Rankings: 4.643
ISI Accession Number ID
Funding AgencyGrant Number
HKU201011159115
Funding Information:

This research is supported in parts by the Seed Funding Programme for Basic Research (201011159115) of HKU.

References

 

DC FieldValueLanguage
dc.contributor.authorWong, TKFen_HK
dc.contributor.authorWan, KLen_HK
dc.contributor.authorHsu, BYen_HK
dc.contributor.authorCheung, BWYen_HK
dc.contributor.authorHon, WKen_HK
dc.contributor.authorLam, TWen_HK
dc.contributor.authorYiu, SMen_HK
dc.date.accessioned2011-09-23T06:19:23Z-
dc.date.available2011-09-23T06:19:23Z-
dc.date.issued2011en_HK
dc.identifier.citationBioinformatics, 2011, v. 27 n. 15, p. 2151-2152en_HK
dc.identifier.issn1367-4803en_HK
dc.identifier.urihttp://hdl.handle.net/10722/140790-
dc.description.abstractMotivation: 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. 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. © The Author 2011. Published by Oxford University Press. All rights reserved.en_HK
dc.languageengen_US
dc.publisherOxford University Press. The Journal's web site is located at http://bioinformatics.oxfordjournals.org/en_HK
dc.relation.ispartofBioinformaticsen_HK
dc.subject.meshAlgorithms-
dc.subject.meshInternet-
dc.subject.meshRNA, Untranslated - genetics-
dc.subject.meshSequence Alignment - methods-
dc.subject.meshSequence Analysis, RNA - methods-
dc.titleRNASAlign: RNA structural alignment systemen_HK
dc.typeArticleen_HK
dc.identifier.emailLam, TW:twlam@cs.hku.hken_HK
dc.identifier.emailYiu, SM:smyiu@cs.hku.hken_HK
dc.identifier.authorityLam, TW=rp00135en_HK
dc.identifier.authorityYiu, SM=rp00207en_HK
dc.description.naturelink_to_subscribed_fulltext-
dc.identifier.doi10.1093/bioinformatics/btr338en_HK
dc.identifier.pmid21659321-
dc.identifier.scopuseid_2-s2.0-79960419898en_HK
dc.identifier.hkuros192201en_US
dc.relation.referenceshttp://www.scopus.com/mlt/select.url?eid=2-s2.0-79960419898&selection=ref&src=s&origin=recordpageen_HK
dc.identifier.volume27en_HK
dc.identifier.issue15en_HK
dc.identifier.spage2151en_HK
dc.identifier.epage2152en_HK
dc.identifier.eissn1460-2059-
dc.identifier.isiWOS:000292778700021-
dc.publisher.placeUnited Kingdomen_HK
dc.identifier.scopusauthoridWong, TKF=25423289800en_HK
dc.identifier.scopusauthoridWan, KL=43262079200en_HK
dc.identifier.scopusauthoridHsu, BY=43261323200en_HK
dc.identifier.scopusauthoridCheung, BWY=36132876900en_HK
dc.identifier.scopusauthoridHon, WK=7004282818en_HK
dc.identifier.scopusauthoridLam, TW=7202523165en_HK
dc.identifier.scopusauthoridYiu, SM=7003282240en_HK
dc.identifier.citeulike9397215-

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