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

Home Search Comparison Documentations Help Release 1.0 Dec 2005

 Comparing with other tools

RNAMST

RNAMotif [5]

RNABOB
[6]

PatSearch [4]

Palingol
[3]

Riboswitch finder [1]

tRNAscan-SE [2]

Diverse RNA
structures search

Yes Yes Yes Yes Yes - -

High speed search against large amount of sequences

 Yes - - - - Yes Yes

Web interface
with real-time response

 Yes - - - - Yes Yes

Flexible search
with bugle and mispair

 Yes - - - - - -

Accept multiple
RNA description

 Yes - - - - - -



 How efficient RNAMST is?
Here we use the purine riboswitch to query against different size of databases and compare with RNABOB and RNAMotif. The purine riboswitch is a metabolite binding domain within certain mRNAs and involves in modulation of gene expression. The RNA motif description of purine riboswitch is given as below, and the searching time comparison of RNAMST, RNABOB and RNAMotif against the different databases is shown as below figures.

  • RNA motif description of Purine Riboswitch:

h5(5,11) ss(2,6) h5(5,9) ss(5,9,seq=gg$) h3 ss(6,10,seq=^gu) h5(4,8) ss(5,9,seq=^cc) h3 ss(2,6) h3

  • Time cost comparison with RNAMotif :

 How flexible RNAMST is?
In addition to fast motif search, supporting bulge constraint is the other major advantage of RNAMST. Since bugle occurs ubiquitously and very often in RNA secondary structure, it should be supported in RNA structure homologs search. For example, searching similar long hairpin - Figure 1.A, RNAMotif only finds results with symmetrical mispair (Figure 1.B) but failure with asymmetrical mispair (Figure 1.D) and bulge (Figure 1.C and E) despite all of them are very similar. But RNAMST have ability to find all of these structural homologs.

Figure 1. Similar RNA 2nd structures. While looking for the structure homologs of A,
RNAMotif only find the B structural homologs, but RNAMST find the all of these structural homologs.

 References

1.          Bengert, P. and T. Dandekar, Riboswitch finder--a tool for identification of riboswitch RNAs. Nucleic Acids Res, 2004. 32(Web Server issue): p. W154-9.2.        

2.         The tRNAscan-SE, snoscan and snoGPS web servers for the detection of tRNAs and snoRNAs. Peter Schattner, Angela N. Brooks1 and Todd M. Lowe. Nucleic Acids Research, 2005, Vol. 33, Web Server issue

3.         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.

4.         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.

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

6.          Http://selab.wustl.edu/cgi-bin/selab.pl?mode=software#rnabob


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