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
Academic Staff Member
Bioinformatics
Institute for Biochemistry and Biology
University of Potsdam
Potsdam,Germany