期刊
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
卷 14, 期 3, 页码 6144-6156出版社
MDPI AG
DOI: 10.3390/ijms14036144
关键词
ncRNAs; rRNAs; multiple sequence alignment (MSA); structural alignment; secondary structure; consensus structures; web server
资金
- MEXT KAKENHI [24680031, 30356357]
- Grants-in-Aid for Scientific Research [24680031, 221S0002, 22240031, 25240044] Funding Source: KAKEN
Due to the recent discovery of non-coding RNAs (ncRNAs), multiple sequence alignment (MSA) of those long RNA sequences is becoming increasingly important for classifying and determining the functional motifs in RNAs. However, not only primary (nucleotide) sequences, but also secondary structures of ncRNAs are closely related to their function and are conserved evolutionarily. Hence, information about secondary structures should be considered in the sequence alignment of ncRNAs. Yet, in general, a huge computational time is required in order to compute MSAs, taking secondary structure information into account. In this paper, we describe a fast and accurate web server, called CentroidAlign-Web, which can handle long RNA sequences. The web server also appropriately incorporates information about known secondary structures into MSAs. Computational experiments indicate that our web server is fast and accurate enough to handle long RNA sequences. CentroidAlign-Web is freely available from http://centroidalign.ncrna.org/.
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