Just for your information.

Nature, 452, 88-92 (2008)

See Supplementary Methods and Discussion,

        6. Transposable elements

thanks atsushi, it will be help, but I need a more suitable and detail protocol for identification of transposons in bacterial genomes 

If you mean in a sequenced genome, I used ISsaga toolkit (http://issaga.biotoul.fr/ISsaga/issaga_index.php).

Hi, I don't know how it works on bacterial genomes, but you could use some tools like RepeatScout or RepeatModeler.

REPET pipeline works like charme in eukaryotic genomes, not surprising to work as well in prokaryotic genomes too. Give it a try and let me know your results.

Quesneville H, Bergman CM, Andrieu O, Autard D, Nouaud D, et al. (2005)

Combined evidence annotation of transposable elements in genome sequences.

PLoS Comput Biol 1: e22. doi:10.1371/journal.pcbi.0010022.

Flutre T, Duprat E, Feuillet C, Quesneville H (2011) Considering transposable

element diversification in de novo annotation approaches. PLoS ONE 6: e16526.

doi:10.1371/journal.pone.0016526.

I think we need to now a bit more details about your project here. What is the bacterium you're working with? Do you want to isolate the Tns experimentally or find them by genome sequence analysis? Mating out assay is the easiest experimental way to go, but you need to have a conjugative plasmid, a conjugation assay and selection markers (that may or may not be naturally present on the Tns) etc.

thanks Youssar, I will have a try

To Toussaint: thanks for your reply. I just want to identify the Tns by sequence analysis, in some bacterial pathogens in clinic.

Are these completed genomes or draft genomes? If it is a completed genome, any of the above mentioned tools would work. If these are draft genomes, you may not be able to reliably estimate the copy numbers, as depending on the sequencing library type , assembly across repeats might not occur. If the raw reads are available one could estimate the copy number based on coverage.

Completely agree with Prerak Desai. In any case one possible way to go is to chose one transposase protein sequence for each family in the ISFinder database (https://www-is.biotoul.fr/) and Tn7 DDE_recombinase/transposase amino-acid sequence (because I think Tn7 is not in that DB which is an IS sequence repository, IS which I consider as transposons as well) and blast it against a translated version  of your genomic sequence. Then you can walk around the transposase hits to look for other expected features (resolvase gene, terminal repeats, resistance genes etc.; be careful that Tns can be VERY long!). There are tools to search for genomic and pathogenicity islands (see http://www.brinkman.mbb.sfu.ca/ for instance) that could also be useful. And for some Tns (integrons, Tn4371-like) there are also typical protein sequences that can be used (tyrosine recombinase/integrase for integrons, see Ryan MP, Pembroke JT, Adley CC 2009 for instance for Tn4371 family and attached). But again, the useful tools can only be defined knowing what is your starting material, and what you're exactly looking for (pathogenicity, resistance determinants etc.).

Chapter The Tn4371 ICE Family of Bacterial Mobile Genetic Elements

thank you Ariane Toussaint. So, identification of transposons still need manually check, it's really a sad news as I will analyze Tns in tens of genomes...

Indeed I'm afraid there isn't any robust prediction tool. But you could use several tools and make a comparison between the predictions for instance. You could combine those methods with genome comparison tools (provided you have closely related genomes of course). These will pick up regions that have insertions-deletions but again it will need manual inspection afterwards to see what is in the identified regions

I think ISFinder has a genome analysis tool for predicting IS but I'm afraid it only works on completely assembled genomes (one if not the main reason being that IS seriously compromise assembly when present in several copies and are lying at ends of contigs, incomplete)!