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Updated: May 14, 2026
08:35
Identification of Alternative Splicing and Polyadenylation in RNA-seq Data
Published on: June 24, 2021
KuPID: Kmer-based Upstream Preprocessing of Long Reads for Isoform Discovery
Molly Borowiak1, Yun William Yu1
1Carnegie Mellon University, Pittsburgh PA 15213, USA.
Biorxiv : the Preprint Server for Biology
|May 13, 2026
Summary
KuPID is a novel method for preprocessing RNA sequencing reads to improve the discovery of new protein isoforms. This kmer sketching approach enhances accuracy and reduces runtime for isoform discovery pipelines.
Area of Science:
- Genomics
- Molecular Biology
- Bioinformatics
Background:
- Eukaryotic genes generate diverse protein isoforms through alternative splicing.
- Current novel isoform discovery methods rely on exon splice junction identification from RNA sequencing (RNAseq) data.
- Accurate splice junction annotation often requires computationally intensive dynamic programming alignment.
Purpose of the Study:
- To introduce KuPID, a preprocessing method for long RNAseq reads.
- To enhance the identification of novel isoform transcripts.
- To improve the efficiency and accuracy of isoform discovery pipelines.
Main Methods:
- KuPID employs kmer sketching as a pre-filtering strategy.
- It rapidly pseudo-aligns reads to known reference isoforms.
- Full alignment is reserved for reads critical to isoform discovery, reducing computational load.
Main Results:
- KuPID preprocessing significantly increases the F1 accuracy of isoform discovery pipelines by up to 16.7 points.
- Runtime is decreased by a factor of 2-3x.
- An optional mode supports both transcript quantification and isoform discovery.
Conclusions:
- KuPID offers a faster and more accurate approach to novel isoform discovery.
- The method effectively filters extraneous reads, improving downstream analysis.
- KuPID represents a valuable tool for genomic and transcriptomic research.
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