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
Galaxy has a few tools which can search for simple repeats.
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
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!
Hello! I've simply asked your question in google:
I received the following answer:
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.
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
There is another useful site for inverted repeat search.
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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.