Question: tBLASTn - How do I turn all repetitive masking off??
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gravatar for molly77
5 days ago by
molly7710
molly7710 wrote:

Hi,

With tBLASTn v2.7.1+ on the command line: I'm using a transcriptome as my nucleotide database and using translated queries that are highly repetitive (these queries sequences have come from my transcriptome so I know they are there), and I'm not getting any hits.

How do I go about generating hits using repetitive queries to identify repetitve fragments in my transcriptome??? I used the "soft_masking false" parameter but it doesn't help. How do I turn off all forms of masking?

I have Google'd this for what seems like hours and cannot find any answers. The BLAST manual isn't that informative and can be confusing.

Thanks!

tblastn blast rna-seq assembly • 61 views
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