Sequence Alignment and lncRNA Discovery at Stockholm University
From September 1 to October 24, 2025, Fabio Zanarello, LongTREC Doctoral Candidate at the Centre for Genomic Regulation (CRG), had the opportunity to carry out a research secondment at Stockholm University, supervised by Kristoffer Sahlin. This secondment offered valuable growth, both in scientific expertise and personal development.
My goal? Acquiring knowledge in sequence alignment and comparison for gene discovery from long-read transcriptomics data. This covered aligning long RNA reads to multiple species, exploring computationally efficient sequence similarity metrics, and optimising alignment of reads from lncRNA genes.
Fabio reflects on his experience:
What I Learned ๐
The stay was highly beneficial for learning fundamental sequence analysis techniques such as sketching, hashing and seeding.
Takeaways ๐ฑ
Quality control and data preparation required a more in-depth analysis than anticipated. As a result, optimising lncRNA-specific alignment was not addressed in practice, though it was discussed with the local LongTREC fellow.
Impact ๐
The secondment produced a comparison of annotation transfer approaches based on read or gene cross-mapping, a set of candidate conserved lncRNA genes across 7 Lepidoptera species, and a set of curated and corrected long RNA reads obtained with tools developed in the host lab. These results advance my main project on lncRNA gene discovery.
Overall, this secondment built my foundation in sequence analysis and moved my lncRNA project forward.
