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detection of inverted repeats of transposons in Bacteria

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?

sequence transposon inverted repeats
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updated by Mensur Dlakic Mensur Dlakic • written by bas1993 • bas1993

1 answer

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.

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written by Mensur Dlakic Mensur Dlakic

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