- a fasta class to make genomic sliding window for the if you have a binding site and you want to prepare the motifs for the binding site as a sliding window you can also use the same.
- You can also search the sliding window motifs starting with the particular tag to see how many of them are generated.
- This has been published as a gem FastaMotifSlidingGenerator
fast = FastaMotifSlidingGenerator.new("ATATAGTATATATA", "3", "GT")
#<#<Class:0x0000000103e98e88>::FastaGenerator:0x0000000103f2e9d8
#@fasta="ATATAGTATATATA", @take=3, @motif="GT">
fast.sequencechunk
["ATA", "TAT", "ATA", "TAG", "AGT", "GTA",
"TAT", "ATA", "TAT", "ATA", "TAT", "ATA"]
fast.returnmotif
["GTA"]
to install
gem install fasta_motif_sliding_generator
require "fasta_motif_sliding_generator"
Gaurav Sablok
University of Potsdam
Potsdam,Germany