Article: RNASAlign: RNA structural alignment system
| Title | RNASAlign: RNA structural alignment system | ||||
|---|---|---|---|---|---|
| Authors | Wong, TKF1 Wan, KL1 Hsu, BY2 Cheung, BWY1 Hon, WK2 Lam, TW1 Yiu, SM1 | ||||
| Issue Date | 2011 | ||||
| Publisher | Oxford 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?] DOI: http://dx.doi.org/10.1093/bioinformatics/btr338 | ||||
| Abstract | 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. 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. | ||||
| ISSN | 1367-4803 2011 Impact Factor: 5.468 2011 SCImago Journal Rankings: 1.118 | ||||
| DOI | http://dx.doi.org/10.1093/bioinformatics/btr338 | ||||
| ISI Accession Number ID | WOS:000292778700021
Funding Information: This research is supported in parts by the Seed Funding Programme for Basic Research (201011159115) of HKU. | ||||
| References | References in Scopus | ||||
| Grants | Indexing data structures for searching ncRNAs |
| dc.contributor.author | Wong, TKF | ||||
|---|---|---|---|---|---|
| dc.contributor.author | Wan, KL | ||||
| dc.contributor.author | Hsu, BY | ||||
| dc.contributor.author | Cheung, BWY | ||||
| dc.contributor.author | Hon, WK | ||||
| dc.contributor.author | Lam, TW | ||||
| dc.contributor.author | Yiu, SM | ||||
| dc.date.accessioned | 2011-09-23T06:19:23Z | ||||
| dc.date.available | 2011-09-23T06:19:23Z | ||||
| dc.date.issued | 2011 | ||||
| dc.description.abstract | 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. 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.grant | Indexing data structures for searching ncRNAs | ||||
| dc.description.grantcode | 104375 | ||||
| dc.description.nature | Link_to_subscribed_fulltext | ||||
| dc.identifier.citation | Bioinformatics, 2011, v. 27 n. 15, p. 2151-2152 [How to Cite?] DOI: http://dx.doi.org/10.1093/bioinformatics/btr338 | ||||
| dc.identifier.citeulike | 9397215 | ||||
| dc.identifier.doi | http://dx.doi.org/10.1093/bioinformatics/btr338 | ||||
| dc.identifier.epage | 2152 | ||||
| dc.identifier.hkuros | 192201 | ||||
| dc.identifier.isi | WOS:000292778700021
Funding Information: This research is supported in parts by the Seed Funding Programme for Basic Research (201011159115) of HKU. | ||||
| dc.identifier.issn | 1367-4803 2011 Impact Factor: 5.468 2011 SCImago Journal Rankings: 1.118 | ||||
| dc.identifier.issue | 15 | ||||
| dc.identifier.pmid | 21659321 | ||||
| dc.identifier.scopus | eid_2-s2.0-79960419898 | ||||
| dc.identifier.spage | 2151 | ||||
| dc.identifier.uri | http://hdl.handle.net/10722/140790 | ||||
| dc.identifier.volume | 27 | ||||
| dc.language | eng | ||||
| dc.publisher | Oxford University Press. The Journal's web site is located at http://bioinformatics.oxfordjournals.org/ | ||||
| dc.publisher.place | United Kingdom | ||||
| dc.relation.ispartof | Bioinformatics | ||||
| dc.relation.references | References in Scopus | ||||
| dc.subject.mesh | Algorithms | ||||
| dc.subject.mesh | Internet | ||||
| dc.subject.mesh | RNA, Untranslated - genetics | ||||
| dc.subject.mesh | Sequence Alignment - methods | ||||
| dc.subject.mesh | Sequence Analysis, RNA - methods | ||||
| dc.title | RNASAlign: RNA structural alignment system | ||||
| dc.type | Article |
Author Affiliations
- The University of Hong Kong
- National Tsing Hua University