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Related Concept Videos

RNA-seq03:21

RNA-seq

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Related Experiment Video

Updated: Apr 20, 2026

Determining 3'-Termini and Sequences of Nascent Single-Stranded Viral DNA Molecules during HIV-1 Reverse Transcription in Infected Cells
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BAsE-Seq: a method for obtaining long viral haplotypes from short sequence reads.

Lewis Z Hong, Shuzhen Hong, Han Teng Wong

    Genome Biology
    |November 20, 2014
    PubMed
    Summary

    Barcode-directed Assembly for Extra-long Sequences (BAsE-Seq) enables long haplotype reconstruction from short-read sequencing. This method accurately identifies viral haplotypes, offering insights into disease evolution and quasispecies dynamics.

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    Amplification, Next-generation Sequencing, and Genomic DNA Mapping of Retroviral Integration Sites

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    Area of Science:

    • Genomics
    • Molecular Biology
    • Virology

    Background:

    • Accurate reconstruction of long DNA sequences, or haplotypes, is crucial for understanding genetic variation and disease.
    • Existing short-read sequencing technologies face limitations in resolving long-range genomic structures.

    Purpose of the Study:

    • To introduce a novel method, Barcode-directed Assembly for Extra-long Sequences (BAsE-Seq), for generating long haplotypes using short-read sequencing.
    • To evaluate the accuracy and applicability of BAsE-Seq for analyzing viral populations.

    Main Methods:

    • BAsE-Seq involves transposing template-specific barcodes onto random DNA segments.
    • Barcoded short reads are then computationally assembled into complete haplotypes.
    • The method was applied to mixed clones of hepatitis B virus and a clinical sample.

    Main Results:

    • BAsE-Seq successfully generated haplotypes exceeding 3 kb in length.
    • The method accurately identified hepatitis B virus haplotypes at frequencies as low as 0.4% with >99.9% specificity.
    • Analysis of a clinical sample yielded over 9,000 viral haplotypes, revealing detailed hepatitis B virus population structure.

    Conclusions:

    • BAsE-Seq is a powerful tool for reconstructing long haplotypes from short-read data.
    • The method provides an unprecedented view of viral population dynamics during infection.
    • BAsE-Seq is suitable for monitoring viral quasispecies evolution in various diseases.