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I want to recreate the UGENE workflow proposed in Convergence of retrotransposons in oomycetes and plants. After being able to understand the data and hmmsearch Here and Here and getting most of the result I want to try to recreate the workflow in UGENE.

I manged to implement the workflow for the search Ugene hmm search Workflow However in the latter parts I struggle to implement the steps of the algorithm

sequences surrounding the regions of significant similarity to the aRNH profile were expanded, when possible, to 10,000 bp in both directions

  • How can sequences expanded in UGENE?
  • How can implement the next steps also? for step three

Third, the enlarged sequences were screened for the presence of significant similarity to RT domains of non-LTR-RTs and LTR-RTs HMM profiles using hmmsearch.

I assume it is very simmilar to the first step in building the right profile and running hmmsearch but the following steps are still unclear to me.

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  • $\begingroup$ Expanding means looking outside the original sequence (in this case by 10kb), so you need to find the position of the sequences and look in the genome for a larger range. Could you clarify what problems do you have with the step three? To me it means to use hmmsearch with specific profiles to search in those sequences $\endgroup$
    – llrs
    Dec 14, 2017 at 8:10
  • $\begingroup$ Well I thought that the search result of step one returns the loction of aRNH then from that location expand in the old data by 10k bp and hmmsearh with the new LTR-RT and non-LTR-RT profiles. but how is the exapnsion from the search result done that was unclear to me. $\endgroup$
    – A.Dumas
    Dec 14, 2017 at 9:58

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