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Related Experiment Video

Updated: Apr 20, 2026

Leveraging CyVerse Resources for De Novo Comparative Transcriptomics of Underserved Non-model Organisms
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VTBuilder: a tool for the assembly of multi isoform transcriptomes.

John Archer1, Gareth Whiteley2, Nicholas R Casewell3

  • 1Department of Parasitology, Liverpool School of Tropical Medicine, Pembroke Place, Liverpool, L3 5QA2, UK. john.archer.jpa@gmail.com.

BMC Bioinformatics
|December 4, 2014
PubMed
Summary

VTBuilder accurately reconstructs complex transcriptomes, overcoming limitations of existing tools for analyzing DNA sequencing reads. This new method improves transcript utility for diverse research fields like transcriptomics and phylogenetics.

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Area of Science:

  • Transcriptomics
  • Bioinformatics
  • Genomics

Background:

  • Millions of short DNA fragments (reads) require assembly into transcript sequences for utilization in research.
  • Current assembly software struggles with isoform variation, leading to incomplete variant identification or chimeric transcripts.
  • Existing methods disrupt relationships between co-evolving sites, limiting downstream analysis.

Purpose of the Study:

  • To introduce VTBuilder, a novel tool for constructing non-chimeric transcripts from complex isoform data.
  • To address the challenges of accurately assembling transcriptomes with isoform diversity.

Main Methods:

  • VTBuilder was validated using simulated reads from Sanger sequenced transcripts (SSTs) of the saw scaled viper, Echis ocellatus.
  • The venom gland transcriptome of the African puff adder, Bitis arietans, was assembled using real-world Illumina MiSeq paired-end reads.
  • The tool was implemented in Java and is available under the GPL GPU V0.3 license.

Main Results:

  • VTBuilder constructed 55 transcripts from simulated reads, with 50 showing >99% similarity to 48 SSTs.
  • In contrast, the Trinity assembler produced only 14 transcripts with similar sequence identity to 11 SSTs.
  • VTBuilder generated transcripts of comparable length to SSTs, while Trinity's were shorter; real-world data assembly recovered all major toxin genes.

Conclusions:

  • VTBuilder maintains relationships between co-evolving sites, enhancing transcript utility for transcriptomics, phylogenetics, and parasite monitoring.
  • Improved transcript assembly quality from read data will benefit future studies.
  • VTBuilder offers a scalable solution for reconstructing complex transcriptomes with isoform diversity.