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Article: RNASAlign: RNA structural alignment system
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TitleRNASAlign: RNA structural alignment system
 
AuthorsWong, TKF1
Wan, KL1
Hsu, BY2
Cheung, BWY1
Hon, WK2
Lam, TW1
Yiu, SM1
 
Issue Date2011
 
PublisherOxford University Press. The Journal's web site is located at http://bioinformatics.oxfordjournals.org/
 
CitationBioinformatics, 2011, v. 27 n. 15, p. 2151-2152 [How to Cite?]
DOI: http://dx.doi.org/10.1093/bioinformatics/btr338
 
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.
 
ISSN1367-4803
2013 Impact Factor: 4.621
 
DOIhttp://dx.doi.org/10.1093/bioinformatics/btr338
 
ISI Accession Number IDWOS:000292778700021
Funding AgencyGrant Number
HKU201011159115
Funding Information:

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

 
ReferencesReferences in Scopus
 
DC FieldValue
dc.contributor.authorWong, TKF
 
dc.contributor.authorWan, KL
 
dc.contributor.authorHsu, BY
 
dc.contributor.authorCheung, BWY
 
dc.contributor.authorHon, WK
 
dc.contributor.authorLam, TW
 
dc.contributor.authorYiu, SM
 
dc.date.accessioned2011-09-23T06:19:23Z
 
dc.date.available2011-09-23T06:19:23Z
 
dc.date.issued2011
 
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.
 
dc.description.naturelink_to_subscribed_fulltext
 
dc.identifier.citationBioinformatics, 2011, v. 27 n. 15, p. 2151-2152 [How to Cite?]
DOI: http://dx.doi.org/10.1093/bioinformatics/btr338
 
dc.identifier.citeulike9397215
 
dc.identifier.doihttp://dx.doi.org/10.1093/bioinformatics/btr338
 
dc.identifier.eissn1460-2059
 
dc.identifier.epage2152
 
dc.identifier.hkuros192201
 
dc.identifier.isiWOS:000292778700021
Funding AgencyGrant Number
HKU201011159115
Funding Information:

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

 
dc.identifier.issn1367-4803
2013 Impact Factor: 4.621
 
dc.identifier.issue15
 
dc.identifier.pmid21659321
 
dc.identifier.scopuseid_2-s2.0-79960419898
 
dc.identifier.spage2151
 
dc.identifier.urihttp://hdl.handle.net/10722/140790
 
dc.identifier.volume27
 
dc.languageeng
 
dc.publisherOxford University Press. The Journal's web site is located at http://bioinformatics.oxfordjournals.org/
 
dc.publisher.placeUnited Kingdom
 
dc.relation.ispartofBioinformatics
 
dc.relation.referencesReferences in Scopus
 
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 system
 
dc.typeArticle
 
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<contributor.author>Cheung, BWY</contributor.author>
<contributor.author>Hon, WK</contributor.author>
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<contributor.author>Yiu, SM</contributor.author>
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Author Affiliations
  1. The University of Hong Kong
  2. National Tsing Hua University