Given one fasta sequence, creates multifasta files containing mutant fasta sequences.
Given one fasta sequence, creates multifasta files containing mutant fasta sequences The script allows only point mutations. See EMBOSS::msbar (not R) for more complex mutation schemes.
e.g. Fasta1_MR0.01_Nmut100.fasta means
Fasta1 original name
MR0.01 mutation rate of 0.01 = 1% = (seqlength of 100 bases x 0.01 = 1 point mutation was introduced)
Nmut100 100 mutated sequences. (the number at the end of each fasta header indicates the mutant id e.g. …._1, …_2
"Caution: Cannot create non-redundant mutants for Fasta1.txt and MR=0.01sequence= 622!!!" This indicates that the algorithm could not find a unique mutant (the same mutants occur at least twice in this set) Change "Ntries" to make more (lengthier) search of unique sequences.
FILES = c("Fasta1.txt")
MutationRate = c(0.01,0.02,0.03,0.05,0.10)
Nmutants = 100 # number of mutated fasta sequences to create
Ntries= 10 # how many times to try searching for a new sequence of a variant?