RF00031 SECIS Selenocysteine insertion sequence more detail ...
CisReg- A set of structured cis-regulatory elements located in mRNA sequences, and flanking regions.
Published in Lange and Maticzka et al., "Global or local? Predicting secondary structure and accessibility in mRNAs", Submitted to NAR Oct 2011
CisReg 1.0 data was processed in May 2011 from Rfam 10.0 Data curation by: Sita J. Lange (1) Joshua N. Gagnon (2) Chris M. Brown (2) . It was used for the development of the LocalFold algorithm.
(1) Department of Computer Science, Albert-Ludwigs-University, Freiburg, Germany
(2) Department of Biochemistry and Genetics Otago, University of Otago, Dunedin, New Zealand
Contact chris.brown at otago.ac.nz
Seed families have been carefully selected from the Rfam database (version 10.0) have been filtered to optimise the quality of sequences. The consensus structures for each seed has been mapped to each single sequence in the seed alignment and then folded using the mapped consensus structure as a constraint using RNAfold. Alignment, family, sequence and structure information is saved in separate files.
The RFxxxxx. struct files (e.g. RF00032.struct) are the key file used for benchmarking structure prediction. These files include all the information to evaluate how well the final structure for the element fits to the consensus structure of the family. According to these values, the best candidates can be chosen for the evaluation of structure prediction programs, etc.
Download the complete set described in the documentation (Download)