Accelerating de novo SINE annotation in plant and animal genomes

Genome annotation is an important but challenging task. Accurate identification of short interspersed nuclear elements (SINEs) is particularly difficult due to their lack of highly conserved sequences. AnnoSINE is state-of-the-art software for annotating SINEs in plant genomes, but it is not available for animals and computationally inefficient for large genomes. Therefore, we propose AnnoSINE\_v2, which extends accurate SINE annotation for animal genomes with greatly optimized computational efficiency. Our results show that AnnoSINE\_v2’s annotation of SINEs has over 20% higher F1-score compared to the existing tool on animal genomes, and is estimated to be more than two orders of magnitude faster on zebrafish and hyena genomes compared to the original AnnoSINE. AnnoSINE_v2 is freely available on Conda and GitHub: . ### Competing Interest Statement The authors have declared no competing interest. * SINEs : Short interspersed nuclear elements pHMMs : profile hidden Markov models