Hi,
I have a small set of genomes from one bacterial species. The genomes differ from each other in that some have been sequenced long ago, e.g. sanger sequenced, while others are new and have been assembled with MiSeq.
Using the latest approaches requires that I use the 'raw' sequencing reads, which is not possible for the older genomes. A tool like ISmapper
An older tool like, ISfinder, can take fasta files with protein sequences and identifies which genes are part of a IS element. But the output is a webbased results. I tried the ISaga page, but that is currently broken.
I have tried to run OASIS, but the biopython needed for that tool is outdated and not available on our computing cluster. So that is a no-go.
So my question: Are there any other options available to detect IS elements from bacterial genome sequences?
Best
Thomas
Hello Thomas,
One caveat for using WGS-based genotyping is a difficulty of data standardization and integration into an accessible databases. most approachs are based on genome-wide gene-by-gene or seq-by-seq analysis. It depends on your Is element and flanking region (Direct repeat of xx bp).
A classical approach is to align your IS element to your reference and trim the flanking regions (max 10 mers). as done in this publication for IS6110 in M. tuberculosis
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4517164/
Or to use a non-free software like RidomSphere+ succesfully applied for M. tb , S. pneumo, E. coli. ..
http://jcm.asm.org/content/52/7/2479.full
Hey Thanks Hafid for the answer. I will look at your suggestions.
Have you tried ISseeker? c.f., https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5343135/