RNA MST  —  An efficient and flexible search tool for RNA structural homologs.

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 RNAMST: A fast and efficient RNA structure search tool
We develop a tool RNAMST which takes advantage of preprocessing strategy to improve the efficiency of RNA motif search against huge amount of sequences. For each sequence, RNAMST will create an indexed file annotating structural information previously. Therefore, RNAMST is capable of searching RNA secondary structures including hairpin, internal loop as well as multi-branch loop rapidly against huge amount of sequences. RNAMST accpets four different kinds of query formats to facilitate user to describe an RNA structure . In addition, the sequences in Rfam, UTRdb, UTRs of Ensembl and UniGene had been indexed by our preprocessing. Through our web interface, the user could easily use RNAMST  and obtain the results and related information quickly .

 System flow of RNAMST web server
Some indexed databases are provided on website such as UTRdb, Rfam, UniGene, and etc. User could describe the RNA motif description and choose the indexed RNA databases through our user friendly interface. The search result could be display on the webpage. The web data flow of RNAMST is drawn below.

 System Limitations

As mentioned before, RNAMST pre-calculated possible hairpin structures. Presently, RNAMST only stores the length of hairpin stem within 3~30 and the length of hairpin loop within 3~2*(length of hairpin stem). For example, if you want to search a structure with hairpin stem length = 3 and hairpin loop length = 10, RNAMST will find nothing (cause of 10 > 2*3; loop length is too long). In the future, RNAMST will calculate and store bigger/longer hairpin structures in our indexed sequence database to reduce these limitations.

 References

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5.         Eddy, S.R., Computational genomics of noncoding RNA genes. Cell, 2002. 109(2): p. 137-40.

6.         Gray, N.K. and M. Wickens, Control of translation initiation in animals. Annu Rev Cell Dev Biol, 1998. 14: p. 399-458.

7.         el-Mabrouk, N. and F. Lisacek, Very fast identification of RNA motifs in genomic DNA. Application to tRNA search in the yeast genome. J Mol Biol, 1996. 264(1): p. 46-55.

8.         Billoud, B., M. Kontic, and A. Viari, Palingol: a declarative programming language to describe nucleic acids' secondary structures and to scan sequence database. Nucleic Acids Res, 1996. 24(8): p. 1395-403.

9.         Grillo, G., et al., PatSearch: A program for the detection of patterns and structural motifs in nucleotide sequences. Nucleic Acids Res, 2003. 31(13): p. 3608-12.

10.       Macke, T.J., et al., RNAMotif, an RNA secondary structure definition and search algorithm. Nucleic Acids Res, 2001. 29(22): p. 4724-35.

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