Tool:retroSeeker: discovering a large set of retrotransposons in humans and any species

Question

[lsp03yjh]

We developed retroSeeker , a new computational software that identifies novel retrotransposons from pairwise alignments of genomes and decodes their biogenesis, expression, evolution and potential functions in humans and other species.

1. We discovered that the majority of new retrotransposons exhibit a specific L1 endonuclease cleavage motif, with some motifs precisely located ten nucleotides upstream of the insertion site.
2. We identified that a large number of candidate functional genes might be generated through a retrotransposition mechanism.
3. Importantly, we uncovered previously uncharacterized classes of retrotransposons related to histone genes, mitochondrial genes and vault RNAs.
4. Moreover, we elucidated the tissue-specific expression of retrotransposons and demonstrated their ubiquitous expression in various cancer types.
5. We also revealed the complex evolutionary patterns of retrotransposons and identified numerous species-specific retrotransposition events.

Taken together, our findings establish a paradigm for discovering novel classes of retrotransposons and elucidating their new characteristics in any species.

Reference

RetroSeeker reveals the characteristics, expression, and evolution of a large set of novel retrotransposons. *Advanced. Biotechnology*. 1, 5 (2023)

New computational approach for the discovery of retrotransposons

Answer 1

[lsp03yjh]

Source Code availability

The source code is written in C/C++ and is accessible at https://github.com/junhong-huang/retroSeeker

[Mensur Dlakic]

The link throws a 404 error. You may want to edit the post and delete the period at the end of GitHub link. Also, explaining a bit better in the repository how to create .net files would be helpful.

[lsp03yjh]

Thank you very much for your comments. I have corrected the GitHub link.