Software.ncrna.org: web servers for analyses of RNA sequences - PubMed
- ️Tue Jan 01 2008
. 2008 Jul 1;36(Web Server issue):W75-8.
doi: 10.1093/nar/gkn222. Epub 2008 Apr 25.
Affiliations
- PMID: 18440970
- PMCID: PMC2447773
- DOI: 10.1093/nar/gkn222
Software.ncrna.org: web servers for analyses of RNA sequences
Kiyoshi Asai et al. Nucleic Acids Res. 2008.
Abstract
We present web servers for analysis of non-coding RNA sequences on the basis of their secondary structures. Software tools for structural multiple sequence alignments, structural pairwise sequence alignments and structural motif findings are available from the integrated web server and the individual stand-alone web servers. The servers are located at http://software.ncrna.org, along with the information for the evaluation and downloading. This website is freely available to all users and there is no login requirement.
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References
-
- Kin T, Tsuda K, Asai K. Marginalized kernels for RNA sequence data analysis. Genome Inform. 2002;13:112–122. - PubMed
-
- Sakakibara Y, Popendorf K, Ogawa N, Asai K, Sato K. Stem kernels for RNA sequence analyses. J. Bioinform. Comput. Biol. 2007;5:1103–1122. - PubMed
-
- Tabei Y, Tsuda K, Kin T, Asai K. SCARNA: fast and accurate structural alignment of RNA sequences by matching fixed-length stem fragments. Bioinformatics. 2006;22:1723–1729. - PubMed
-
- Sakakibara Y. Pair hidden Markov models on tree structures. Bioinformatics. 2003;19:i232–i240. - PubMed
-
- Sato K, Sakakibara Y. RNA secondary structural alignment with conditional random fields. Bioinformatics. 2005;21:ii237–ii242. - PubMed