| layout |
|---|
default_modified |
-
What are the repeat-masking methods that are computationally less expensive than RepeatModler and RepeatMasker, when your goal is masking repetitive sequences to facilitate the whole genome alignment (i.e. you are not interested in the classification, etc. of repeat elements, and a bit of "over-masking" is okay)?
- Hausmann and Kurtz (2021) DeepGRP: engineering a software tool for predicting genomic repetitive elements using Recurrent Neural Networks with attention Algorithms Mol Biol 16:20{:target="_blank"}
- Feng, et al. (2021) Sequence repetitiveness quantification and de novo repeat detection by weighted k-mer coverage Brief Bioinform 22:bbaa086{:target="_blank"}
- Osipova, Hecker, and Hiller (2019) RepeatFiller newly identifies megabases of aligning repetitive sequences and improves annotations of conserved non-exonic elements Gigascience 8:giz132{:target="_blank"}
- Lian, et al. (2016) A Complete and Accurate Ab Initio Repeat Finding Algorithm Interdiscip Sci 8:75-83{:target="_blank"}
- Girgis (2016) Red: an intelligent, rapid, accurate tool for detecting repeats de-novo on the genomic scale BMC Bioinformatics 16:227{:target="_blank"}
- Morgulis, et al. (2006) WindowMasker: window-based masker for sequenced genomes Bioinformatics 15:134-141{:target="_blank"}
(Back to questions or bookmarks)
Always click the large Dong-Ha Oh to go back to main index