genometools/genometools — pull request #32 by satta (2013-07-19 16:23:32+00:00)
Title: add pHMM protein domain search to TIRvish

This commit adds profile HMM search to the experimental TIRvish tool, much similar to the implementation in the LTRdigest tool. It allows for the detection of internal transposase (e.g. DDE) domains inside de novo detected candidates. In addition, a bug in the HMMER3 output parser needed to be fixed, addressing a failed assertion when one of the input models contains a consensus annotation. Some minor accessor functions were added to utility classes as well.