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Question: Retrieving nBLAST similarity hits and flanking regions.
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gravatar for Guilherme Dias
3.6 years ago by
Guilherme Dias • 110
Brazil
Guilherme Dias • 110 wrote:

Hey guys,

I need to retrieve some non-annotated repetitive elements from an assembled genome plus their flanking regions (through nBLAST).
Is there a tool on Galaxy that could help me do that at a faster pace?

Thanks
blast • 840 views
ADD COMMENT • link •
modified 3.6 years ago by Jennifer Hillman Jackson ♦ 25k • written 3.6 years ago by Guilherme Dias • 110
3
gravatar for Jennifer Hillman Jackson
3.6 years ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

A tool such as Repeat Masker could be used. Then once the coordinates are identified, use "Get Flanks". An alternate server from http://usegalaxy.org will be needed for the RM run (another public server, local, or cloud).

Thanks, Jen, Galaxy team
ADD COMMENT • link written 3.6 years ago by Jennifer Hillman Jackson ♦ 25k

Hey Jen, this would be a nice option. Nevertheless, the RM server seems to mask all repeats available in the Repbase library.

So, what if I just want to mask this specific repeat I'm studying?

ADD REPLY • link written 3.6 years ago by Guilherme Dias • 110

If you add the tool to a local/cloud, then you can choose the options just like as if running it line command. Perhaps this will work out for you? Alternatively, you could possibly use the masking tools in the EMBOSS tool suite. These are on Main, if you want to test them out, use the tool search with the keyword "mask" to find them. I haven't tried to use either these on a full genome before, but you could test and time it against BLASTn. Jen

ADD REPLY • link written 3.6 years ago by Jennifer Hillman Jackson ♦ 25k
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