cm_5_8S: Covariance Model for 5.8S rRNA

In brendanf/inferrnal: Interface to Call Programs from Infernal RNA Covariance Model Package

Covariance Model for 5.8S rRNA

Description

This is a convenience function to return the path the RFAM 5.8S rRNA covariance model, for use in cmsearch() or cmalign(). The original file is from https://rfam.xfam.org/family/RF00002/cm.

Usage

cm_5_8S()

Value

(character string) the path to the CM file

Examples

    # search sequences from a fasta file for Rfam RF00002 (5.8S rRNA)
    cm <- cm_5_8S()
    sampfasta <- sample_rRNA_fasta()
    cmsearch(cm = cm, seq = sampfasta, cpu = 1)

brendanf/inferrnal documentation built on Feb. 4, 2023, 4:49 p.m.