Identifying truncated protein domain encoding DNA sequences
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14 months ago
Anand Rao ▴ 430

Is there an off-the-shelf tool or pipeline that will report all protein domain encoding DNA encoding sequences in a given genome, INCLUDING these conditions:

  1. the encoded protein domain is partial or truncated, and / or
  2. the encoding region may be interrupted by one or more introns, and
  3. has the flexibility of using protein profile as query to scan the genome.

I have some amorphous ideas about using fastBlockSearch in AUGUSTUS, and / or PseudoPipe. But I am collecting better crystallized ideas, especially if you've already solved this problem.

Thank you, in advance. Cheers!

protein domain truncation AUGUSTUS fastBlockSearch • 307 views

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