helix: Helices predicted by TRANSAT with p-values

In R4RNA: An R package for RNA visualization and analysis

Description

This data set contains two sets of helices and a multiple sequence alignment. The two sets of helices are helices and known which are helices predicted to occur for RNA sequence RF00458 by the program TRANSAT, and experimentally proposed structure of the same sequence, respectively. fasta is the seed homologues for the multiple sequence alignment obtained from the RFAM database.

Usage

    data(helix)

Format

helix and known are 4 column data frames, where columns i and j denote the left-most and right-most basepairs, the length is the number of consecutive basepairs the helix contains, and the value is assigned to each helix on a row.

fasta is an array of named characters of length 7.

Value

fasta is an array of strings, helix and known are data.frames in “helix” format.

References

Wiebe NJ, Meyer IM. (2010) TRANSAT– method for detecting the conserved helices of functional RNA structures, including transient, pseudo-knotted and alternative structures. PLoS Comput Biol. 6(6):e1000823.

Gardner PP, Daub J, Tate J, Moore BL, Osuch IH, Griffiths-Jones S, Finn RD, Nawrocki EP, Kolbe DL, Eddy SR, Bateman A. (2011) Rfam: Wikipedia, clans and the “decimal” release. Nucleic Acids Res. 39(Database issue):D141-5.

R4RNA documentation built on Nov. 8, 2020, 5:15 p.m.