Predicts Oomycete Effectors
An example of effector.summary output
Returns non-redundant sequences from hmm.search or regex.search and ge...
effectR: An R Package to Call Oomycete Effectors
Converts FASTA to STOCKHOLM
Check if HMMER is installed and return path
Check if MAFFT is installed and return path
Plots the relative frequencies of each position for hmmsearch table.
Searching for motifs using HMM searches
Searching for motifs using regular expressions (REGEX)
Function to run the effectR package using a shiny app
Predicts cytoplasmic effector proteins using genomic data by searching for motifs of interest using regular expression searches and hidden Markov models (HMM) based in Haas et al. (2009) <doi:10.1038/nature08358>.