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.