Multiple alignment using Infernal
Computing a multiple sequence alignment using the Infernal software.
cmalign(in.file, out.file, CM.file, threads = 1)
Name of FASTA-file with input sequences.
Name of file to store the result.
Name of file with correlation model.
Number of CPU's to use
The software Infernal (Nawrocki&Eddy, 2013) must be installed and available on the system. Test
this by typing
system("cmalign -h") in the Console, and some sensible output should be produced.
For more details on Infernal, see http://eddylab.org/infernal/.
This function is most typically used to align 16S rRNA sequences.
cmalign function will produce a multiple alignment, like e.g.
muscle, but makes use
of a correlation model to do so. A correlation model means in this case a description of
how various bases have a long-range relation, due to folding of the sequence. This means that you can
only use this function to align sequences for which you have such correlation models. Such models
are typically available for a number of RNA-families, see below.
CM.file is the name of a file with a valid correlation model, e.g. one downloaded
from the Rfam database (http://rfam.xfam.org/). See examples below for the 16S model supplied with this
The result is written to the file specified in
E.P. Nawrocki and S.R. Eddy, Infernal 1.1: 100-fold faster RNA homology searches, Bioinformatics 29:2933-2935 (2013).
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