When running MITE-hunter, can I split the input genome?

Question

[gerrychang1985]

Hi, everyone,

I was running MITE-hunter on a 600Mb sized genome, but it take too much time when generating the TSD file. Splitting the input genome and running them parallelly might increase the speed, but I noticed that the following steps involved all-by-all blastn. Will the splitted genome affect the blastn and further affect the MITE annotation?

Thank you.

Answer 1

[lieven.sterck]

Yes you should be able to do so.

You make one blastdb of your whole genome, then you split the input file for the blast searches in batches and run those in parallel. Depending on the requested output you will need to correctly concatenate the separate output files you will get.

This approach should not affect the blast result (so will be identical to the 'true' all-vs-all approach)

Answer 2

[Dave Carlson]

Good question. I'm in the same boat. What did you end up deciding to do?

Answer 3

[VS]

I have the same question, did you find an answer to this?