Last modified on 25 January 2016.

Literature Reference:

Macke T.J., Ecker D.J., Gutell R.R., Gautheret D., Case D.A., and Sampath R. (2001).
RNAMotif, an RNA secondary structure definition and search algorithm.
Nucleic Acids Research, 29(22):4724-4735.
[ PM | PMC | DOI ]

Manuscript Figures and Tables:

Description Figure
Figure 1abc: Examples of RNA structure motifs and descriptor constraints with important conserved nucleotides and scoring values.
  1. A helical stem closed by a tetraloop.
  2. An E-loop motif.
  3. The core of the E-loop depicted with the observed non-canonical base pairing interactions.
 JPG
Figure 1d: Examples of RNA structure motifs and descriptor constraints with important conserved nucleotides and scoring values.
  1. E-loop descriptor derived from the constraints shown in (B).
 JPG
Figure 2: Models for the IRE structure and generic descriptor.
  1. IRE bulge model.
  2. IRE internal loop model.
  3. Descriptor that captures both types of IRE.
 JPG
Figure 3: SRP-RNA alignment and structure.
  1. Structure-based alignment of the domain IV stem-loop region of SRP-RNA based on the full-length alignment from the SRP-RNA website.
  2. A consensus diagram of the SRP-RNA structutre derived from analyzing the alignment of over 100 organisms.
 JPG
Figure 4: Summary of results of an RNAMotif search for SRP-RNA.
  1. Score distribution of true and false hits based on RNAMotif scores in a search of the GenBank nucleotide database with an SRP-RNA descriptor.
  2. Summary of scores for true and false hits.
 JPG
Table 1: Conversion of the descriptor structure motifs into an RNAMotif search list. JPG
Table 2: Results of an RNAMotif search for E-loop motifs in E. coli 16S and 23S rRNA sequences. JPG
Table 3: Other rRNA E-loop motifs that were not identified by the RNAMotif descriptor. JPG
Table 4: Perfect matches to IRE motif in human UTR sequences. JPG
Table 5: Identification of SRP-RNA in prokaryotic genome sequences. JPG