Align sequences via clustalo
Align sequences for an object of class LowMACA
an object of class LowMACA containing at least 2 sequences.
a character string that contains the file name where clustal omega alignment file will be stored. In case it's NULL no file will be written. Default=NULL
a character string indicating the email address where error report should be sent in web mode
a character string containing the path to Perl executable. if missing, "perl" will be used as default
When analysing Pfam sequences, it is possible to use the Hidden Markov Model (HMM) of the specific Pfam to align the sequences. Default is FALSE.
When analysing Pfam sequences, use all the genes that belong to the Pfam to generate the alignment. This creates a unique mapping between individual residues and consensus sequence, disregarding the set of sequences that are selected for the analysis. Default is FALSE.
This method launches a system call to clustalo aligner
and optionally creates a fasta file in clustal format.
A warning is returned if at least one sequence has a pairwise similarity below
20% to any other sequence.
If only one sequence is passed to
alignSequences, the alignment will be skipped,
but no warning will be raised.
If mail is not NULL, a local installation of clustal omega
is no longer required and the alignment is
performed using clustal omega EBI web service. A limit of 2000 sequences is set
in this case and perl must be installed in the system
The method returns an object of class LowMACA updating the slot
When a sequence has a similarity below 20%, a warning is raised. In order to produce strong results in terms of conservation of multiple mutations, consider to remove that sequence from the analysis. The alignment will obviously change.
Stefano de Pretis, Giorgio Melloni
1 2 3 4 5 6 7 8 9 10
#Create an object of class LowMACA for RAS domain family lm <- newLowMACA(pfam="PF00071" , genes=c("KRAS" , "NRAS" , "HRAS")) #Align sequences using local installation of clustalo lm <- alignSequences(lm) #Web service clustalomega aligner lm <- alignSequences(lm , mail="firstname.lastname@example.org") #Use HMM to align lm <- alignSequences(lm , use_hmm=TRUE) #Use "datum" lm <- alignSequences(lm , datum=TRUE)
Want to suggest features or report bugs for rdrr.io? Use the GitHub issue tracker.