clustalRNA: alignment of RNA sequences for the spike protein of some...

In geantonicelli/firstPackage: set of wrapper functions for phylogenetic analysis

Description

14 different sequences of some sarbecoviruses closely related to SARSCoV2 were retrieved from public databases and compared using CLUSTAL omega (1.2.4) alignment software with the output in clustal format (see examples section for the complete protocol for retrieving, saving and processing the data)

Usage

clustalRNA

Format

a list of class alignment with 4 elements

nb

number of sequences compared

nam

sequence name (accession number)

seq

a list of RNA sequences

com

NA

Details

1. spikeRNA_annot <- read.csv(system.file('extdata', 'spike_annot.csv', package='firstPackage'))

2. accessions <- spikeRNA_annot$accession

3. download manually each sequence from 'genbank' and save as spike.fasta and perform an alignment with clustal omega with following commands (it needs to be installed locally or use a web interface)

4. clustalo –threads=4 -v –outfmt=clustal -t RNA -i ./data/sequences/spike.fasta -o ./data/sequences/spike_align.aln

5. clustalRNA_load <- load_alignment(system.file('extdata', 'spike_align.aln', package='firstPackage'), 'clustal')

Source

the genbank database of the National Center for Biotechnology Information or the Universal Protein Resource UniProt database

geantonicelli/firstPackage documentation built on Aug. 24, 2020, 3:14 a.m.