Motif Finder
Welcome to Motif Finder! This is a command line utility that allows you to take a FASTA file, specify a few parameters, and (hopefully) get some motifs prevalent in the sequences.
Prerequisites
This utility should work on all platforms if it has been compiled for it. If it hasn't, you can build it for your platform by cloning this repository:
git clone https://github.com/nithishbn/MotifFinder.git
and running
cargo build --release
in the source directory.
This will leave an executable in the target/release/ directory which you can then run in the command line:
motif_finder.exe
Data format
This tool technically accepts all FASTA files, but the way it's meant to be used is to use an interesting approach in motif finding.
RNASeq
By using RNASeq data and aligning it back to a reference genome, we can identify the alignment sites of transcripts. Using these alignment sites, we can generate the set of sequences x bp upstream of the site in which to look for motifs, specifically for transcription factor binding sites.
This method involves finding an organism with RNASeq data, a reference genome, and a few bioinformatics tools including samtools, bamtools, and bedtools.
Examples
You can try to find the motifs present in promoters.fasta, a set of 4 promoters known in P. tricornutum, a relatively unknown diatom species.
Gibbs Sampler
Gibbs Sampler is an algorithm that iteratively searches for the best set of motifs in a set of sequences and throws out motifs at random until all iterations are finished.
motif_finder.exe -i promoters.fasta -e 4 -k 10 -o promotifs.txt gibbs -t 100 -r 100
Randomized Motif Search
Randomized Motif Search is an algorithm that iteratively searches for the best set of motifs in a set of sequences and throws out motifs at random until the score cannot be improved anymore.
motif_finder.exe -i promoters.fasta -e 4 -k 10 -o promotifs.txt randomized -r 100
Median String
Median String is an algorithm that checks the hamming distance from each kmer from each sequence and returns the minimized kmer from all strings. This algorithm is incredibly slow but can result in very accurate but short kmers. Be warned when using large k values.
motif_finder.exe -i promoters.fasta -e 4 -k 8 -o promotifs.txt median