Transposable Elements Database

Question

[holzdan]

Hey !

I've seen there's a big amount of tools for finding transposable elements out there. Unfortunately most are for unix/linux based operating systems. Can somebody recommend a good online search database (or tool for windows) for detecting transposable elements in a given bacterial sequence?

Cheers

[Anima Mundi]

Hi, check out this post. It contains a list of tools to find low complexity regions, maybe there is also something that provides web services for bacteria.

Answer 1

[jotan]

Galaxy has a few tools which can search for simple repeats.

https://usegalaxy.org/

Under Tools -> EMBOSS

equicktandem - Finds tandem repeats

palindrome - Looks for inverted repeats in a nucleotide sequence

etandem - Looks for tandem repeats in a nucleotide sequence

einverted - Finds DNA inverted repeats

[natasha.sernova]

That's fine, but what about bacterial genomes in Galaxy?

How can I find a particular bacteria there?

Sorry, Galaxy is a great collection of different tools, and I can

upload a file from my computer! Perfect, but is it possible for 20 files, a group of bacteria?

Thank you very much!

Answer 2

[natasha.sernova]

Hello! I've simply asked your question in google:

I received the following answer:

https://yandex.ru/yandsearch?&clid=2186621&text=database%20%28or%20tool%20for%20windows%29%20for%20detecting%20transposable%20elements%20in%20a%20given%20bacterial%20sequence&lr=213

I've changed your question a little bit:

(database OR a tool for windows) for detecting transposable elements in a given bacterial sequence

The answer is below, it is a little bit different.

https://www.google.ru/#newwindow=1&q=%28database+OR+a+tool+for+windows%29+for+detecting+transposable+elements+in+a+given+bacterial+sequence

Answer 3

[jotan]

Would RepeatMasker work?

http://www.repeatmasker.org/cgi-bin/WEBRepeatMasker

There's an alternate tool if your species doesn't have a repeat library:

http://www.repeatmasker.org/cgi-bin/RepeatProteinMaskRequest

Answer 4

[natasha.sernova]

There is another useful site for inverted repeat search.

https://tandem.bu.edu/cgi-bin/irdb/irdb.exe?taskid=30

Answer 5

[holzdan]

thanks for your answers. yep im actually also looking for a heuristic search tool (basically scanning for inverted repeats etc.. ) which doesnt need a database as reference...

cheers