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Related Experiment Video

Updated: May 14, 2026

Identification of Alternative Splicing and Polyadenylation in RNA-seq Data
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
PubMed
Summary
This summary is machine-generated.

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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.
Keywords:
RNAseqnovel isoform discoverysketching

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Last Updated: May 14, 2026

Identification of Alternative Splicing and Polyadenylation in RNA-seq Data
08:35

Identification of Alternative Splicing and Polyadenylation in RNA-seq Data

Published on: June 24, 2021

Optimization for Sequencing and Analysis of Degraded FFPE-RNA Samples
07:30

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Published on: June 8, 2020

  • 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.