msfRNA: alignment of RNA sequences for the replicase 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 msf format (see details for the complete protocol for retrieving, saving and processing the data)

Usage

msfRNA

Format

a matrix of class DNAbin

attribute (dimnames)

sequence name (accession number)

Details

1. orf1abRNA_annot <- read.csv(system.file('extdata', 'orf1ab_annot.csv', package='firstPackage'))

2. accessions <- orf1abRNA_annot$accession

3. download manually each sequence from 'genbank' and save as orf1ab.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=msf -t RNA -i ./data/sequences/orf1ab.fasta -o ./data/sequences/orf1ab_align.msf

5. msfRNA_load <- load_alignment(system.file('extdata', 'orf1ab_align.msf', package='firstPackage'), 'msf', 'RNA')

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.