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.
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.