rfamCovarianceModel: Get the covariance model associated to an Rfam family

In rfaRm: An R interface to the Rfam database

Description

Gets the covariance model generated with the Infernal software of the Rfam family. Covariance models can be used in Infernal to search through a list of sequences for high-scoring hits to the models. If a filename is provided, the covariance model will be saved to the specified path.

Usage

rfamCovarianceModel(rfamFamily, filename=NULL)

Arguments

rfamFamily	string with an Rfam family accession or ID for which the covariance model should be retrieved.
filename	string indicating a path to which the covariance model should be written. In the default behaviour, filename=NULL, the covariance model will not be saved into any file, and instead will only be returned as a string.

Value

A string with the covariance model of the Rfam family in the Infernal format. If a filename is provided, the covariance model file will also be written to the specified path.

References

Ioanna Kalvari, Joanna Argasinska, Natalia Quinones-Olvera, Eric P Nawrocki, Elena Rivas, Sean R Eddy, Alex Bateman, Robert D Finn, Anton I Petrov, Rfam 13.0: shifting to a genome-centric resource for non-coding RNA families, Nucleic Acids Research, Volume 46, Issue D1, 4 January 2018, Pages D335–D342, https://doi.org/10.1093/nar/gkx1038

Eric P Nawrocki, Sean R Eddy, Infernal 1.1: 100-fold faster RNA homology searches, Bioinformatics, Volume 29, Issue 22, 15 November 2013, Pages 2933–2935, https://doi.org/10.1093/bioinformatics/btt509

https://docs.rfam.org/en/latest/api.html

http://eddylab.org/infernal/Userguide.pdf

Examples

# Retrieve the covariance model for the Rfam family with ID "FMN" and save it
# to a file

rfamCovarianceModel("FMN", filename="FMNcovarianceModel.cm")

# Retrieve the covariance model for the Rfam family with accession "RF00174" and
# save it to a file

rfamCovarianceModel("RF00174", filename="RF00174covarianceModel.cm")

rfaRm documentation built on March 16, 2021, 6:01 p.m.