sample_data: Sample rRNA sequences

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

Sample rRNA sequences

Description

These are example files based on amplicon sequences from a soil metabarcoding study. sample_rRNA_fasta is a FASTA file of amplicon sequences, sample_rRNA_5_8S a FASTA file of the same amplicons, but including only the 5.8S region, and sample_rRNA_stk is a Stockholm-format alignment of the 5.8S region.

Usage

sample_rRNA_fasta()

sample_rRNA_stk()

sample_rRNA_5_8S()

Value

a path to the sample data 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)

    # read a stockholm alignment
    msafile <- sample_rRNA_stk()
    msa <- read_stockholm_msa(msafile)
    msa

brendanf/inferrnal documentation built on Nov. 26, 2024, 4:24 p.m.