Question: Obtain fasta file of tblastn hits selected by coverage and similarity
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gravatar for TWV
2.1 years ago by
TWV70
TWV70 wrote:

I am trying to identify DNA transposons in a newly sequenced insect. One of the ways to do this is by performing a tblastn of known DNA-transposase proteins towards the genome.

I therefore downloaded a .fasta file with DNA-transposase protein sequences and now want to blast them all to my genome, while selecting for hits that have a coverage of over 50% and a similarity of over 30%.

Then I wish to extract the best hits along with 5kb of flanking region into a .fasta file.

I am new to tblastn and can't figure out how I would go about doing that, can anyone lead me onto the right path?

blast tblastn • 679 views
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