hmm.search: Searching for motifs using HMM searches
Description Usage Arguments Value
Description
This function uses MAFFT and HMMER to search for sequences with protien motifs using hidden markov models.
Usage
1 2 3 | hmm.search(original.seq, regex.seq, alignment.file = NULL,
save.alignment = FALSE, mafft.path = NULL, num.threads = 2,
hmm.tresh = 0, hmm.path = NULL, seed = 12345)
|
Arguments
original.seq |
The absolute path for the original six-frame translation FASTA file |
regex.seq |
A list[1] of objects returns from pattern.search. The HMM profile will be constructed using these sequences |
alignment.file |
The absolute path for an alignment file of the sequences to build the hmmer profile from.It's recommended that the alignment file cointains the same sequences than the ‘regex.seq' files. If the user provides the absolute path, *motiFUN* won’t use MAFFT to align the sequences and will use the alignment for the HMMER searches. If no alignment file is provided, *motifFUN* will use MAFFT to align the sequences from 'regex.seq' and run HMMER. |
save.alignment |
Save the alignment in the returning object. The MAFFT alignment will be saved as the first element of the returned object |
mafft.path |
Local path of folder containing the MAFFT binary executable file or the executable file itself. If not specified, then MAFFT must be in the program search path. |
num.threads |
Number of threads to be used by MAFFT. |
hmm.tresh |
Set the bit score cutoff for the per-sequence ranked hit list to a real number. (Default = 0) |
hmm.path |
Local path of folder containing the HMMER binaries. If not specified, then HMMER executables must be in the program search path. |
seed |
The seed to used with HMMER commands. Set this to get the same output each time. |
Value
Returns total sequence.
@examples
hmm.search(original.seq = fasta.file, regex.seq = PATT_REG, mafft.path = "complete path", hmm.path = "complete path")
