A faster implementation of the string search for the check of the insertion elements if present in the genome string and then clip those insertion sites and get a clean genome. a bacterial insertion element scannner based on the string search algorithm, it will check for the mentioned insertion element pattern and then clip that pattern and will stitch the genome devoid of the insertion elements.It will give you directly the fasta, you can also write the fasta. I am making a insertion element package and associating that to the microbiomes. I also implemented a parallel support.
bacterial_Insertion_Element_Splitter("/Users/gauravsablok/Desktop/CodeBase/check.fasta",
"GCAGCGTACGATATATAT")
Gaurav
Academic Staff Member
Bioinformatics
Institute for Biochemistry and Biology
University of Potsdam
Potsdam,Germany