MiRvestigator_standalone is a project mainly written in Python, it's free.
Stand alone version of miRvestigator HMM that takes as input a FASTA stlyed PSSM file.
Copyright -- Chris Plaisier (4/14/2011) This is a program to identify miRNAs from a Position Specific Scoring Matrix. A PSSM is read from a user specified file and is then passed to miRvestigator which downloads the mature miRNA seed seqeunces from miRbase.org and compares these mature seed sequences against the PSSM. This is accomplished by converting the PSSM into a Hidden Markov Model (HMM), very similar to a profile HMM, and then using the Viterbi algorithm to simultaneously align and calcualte a probabilty for the alighment of the miRNA seed to the HMM. A p-value is calculated by exhaustively comparing all potential miRNA seed sequneces that could bind to 3' UTRs, and using simulations the p-value for the Viterbi probability is the optimal metric for gauging miRNA seed to PSSM similarity.
In order to run this program you will need:
Python (www.python.org) Active internet connection to download latest miRBase release (mature.fa.gz)
For python programs the program file 'miRvestigator_standalone.py' must be prefaced with 'python' in order to run. Thus use the command 'python miRvestigator_standalone.py' to see the command line help:
###############################################################
############################################################### Usage: python miRvestigator_standalone.py -p example.fasta -s hsa -wobble NA -6 N -7 N -8 Y
Options:
-h, --help show this help message and exit
-p PSSMFILE, --pssmFile=PSSMFILE
[Required] Name of the PSSM file entered using a fasta
like format where each motif is named and is followed
with rows A, C, G, T and columns equal to the lenght
of the motif (values in the matrix should be separated
by spaces). The values entered should be probabilities
and the columns should sum to 1.
-s SPECIES, --species=SPECIES
Species code whose miRNAs the PSSMs should be compared
against. Common species codes ( =
If the species being studied is human then you need only specify the pssm file in fasta format. Here is an example fasta pssm entry:
hsa-miR-1 0.80 0.01 0.75 0.01 0.02 0.10 0.05 0.99 0.04 0.85 0.10 0.01 0.10 0.60 0.80 0.00 0.05 0.02 0.10 0.10 0.02 0.20 0.05 0.00 0.11 0.02 0.05 0.88 0.86 0.10 0.10 0.01
If using another species enter the species code. Any species available on miRBase should work with miRvestigator including the most common species:
Wobble base-pairing may be turned on or off by either supplying a minimum frequency (default is 0.25) or not, respecitively. Finally, the 6-, 7- and 8-mer seed models are by default turned on, and by setting them to 'N' they can be turned off.
More than one motif may be input into the miRvestigator HMM stand alone application. The results for each PSSM are placed into a
Thus this provides an alternative to the miRvestigator web server (mirvestigator.systemsbiology.org) if motif are derived using an alternative de novo motif detection algorithm.