Selected article for: "data set and rna structure"
Author: Seemann, Stefan E.; Gorodkin, Jan; Backofen, Rolf
Title: Unifying evolutionary and thermodynamic information for RNA folding of multiple alignments
  • Document date: 2008_10_4
    • ID: wtvfow2f_34
    Snippet: Rfam (40) is the most up-to-date comprehensive and freely accessible RNA structure database, so we used 46 Rfam (version 8.0) seed alignments for parameter tuning and for PETfold benchmarking. Our data set consists of 17 RNA families recommended by refs. (21) and (11) and 29 additional families possessing a high-quality alignment documented by the SARSE project (41) . The alignments of the second set of data are characterized by a score for incon.....
    Document: Rfam (40) is the most up-to-date comprehensive and freely accessible RNA structure database, so we used 46 Rfam (version 8.0) seed alignments for parameter tuning and for PETfold benchmarking. Our data set consists of 17 RNA families recommended by refs. (21) and (11) and 29 additional families possessing a high-quality alignment documented by the SARSE project (41) . The alignments of the second set of data are characterized by a score for inconsistent base pairs 4 and a score for novel base pairs 4. These criteria are satisfied by 43 families, of which two families overlap the first set and 12 were rejected because of an annotated structure with <40% of bases being involved in base pairs. Large alignments were reduced by sequence similarity as in (41) . An overview of all RNA families in the data set is given in Supplementary Table 1 .

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