detection of inverted repeats of transposons in Bacteria

Question

[bas1993]

I found several transposase genes in a bacterial assembly and I now want to determine the size of the insertion sequence. In literature I read that transposons are usually flanked by inverted repeats (>9 bp) and direct repeats.

However, depending on which parameters I use with the tool below (max size inverted repeat or max distance between repeats) it results into many different sized inverted repeats/palindromes. So at the moment I am still not quite sure how to define where my transposon starts and where it ends.

http://emboss.bioinformatics.nl/cgi-bin/emboss/palindrome

Has anyone done something similar and used the same tool or a different one?

Answer 1

[Mensur Dlakic]

A simple palindrome search is not likely to be specific enough, and you will end up sifting through lots of false positives. I suggest using a tool that is specifically meant for this purpose. Here are few links to consider, but I'd invest some time into Google searching for something more recent.

• http://tandem.bu.edu/irf/irf.download.html
• https://www.nature.com/articles/hdy2009165
• https://bioinformaticsonline.com/pages/view/27459/tools-for-searching-repeats-and-palindromic-sequences