sample_rRNA_fasta | R Documentation |
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.
sample_rRNA_fasta() sample_rRNA_stk() sample_rRNA_5_8S()
a path to the sample data file
# 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
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