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Updated: Sep 23, 2025

A Fast and Quantitative Method for Post-translational Modification and Variant Enabled Mapping of Peptides to Genomes

A Fast and Quantitative Method for Post-translational Modification and Variant Enabled Mapping of Peptides to Genomes

Published on: May 22, 2018

PacRAT: a program to improve barcode-variant mapping from PacBio long reads using multiple sequence alignment.

Chiann-Ling C Yeh¹, Clara J Amorosi¹, Soyeon Showman^1,2

¹Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA.

Bioinformatics (Oxford, England)

|May 13, 2022

Summary

This summary is machine-generated.

PacBio sequencing artifacts hinder genetic variant analysis. The new PacBio Read Alignment Tool (PacRAT) improves barcode-variant mapping accuracy, increasing usable reads for downstream applications.

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Area of Science:

Genomics
Bioinformatics
Molecular Biology

Background:

PacBio sequencing is increasingly used for genetic variant characterization.
Existing methods for resolving PacBio sequencing artifacts often lead to inaccurate or unusable reads.

Purpose of the Study:

To develop a tool, PacBio Read Alignment Tool (PacRAT), to enhance the accuracy of barcode-variant mapping in PacBio sequencing data.
To improve the identification and usability of sequencing reads by addressing PacBio-specific artifacts.

Main Methods:

Developed PacRAT, a Python-based tool incorporating advanced read alignment and consensus calling steps.
Simulated PacBio reads from eight variant libraries of varying lengths to quantify performance.
Applied PacRAT to real (non-simulated) PacBio sequencing libraries.

Main Results:

PacRAT demonstrated improved accuracy in pairing barcodes with their corresponding genetic variants across simulated libraries.
Analysis of real sequencing data showed a significant increase in the number of usable reads after applying PacRAT.
The tool effectively resolves common PacBio sequencing artifacts, leading to more reliable data.

Conclusions:

PacRAT offers a robust solution for improving the accuracy and utility of PacBio sequencing data for genetic variant analysis.
The tool enhances downstream analyses by increasing the yield of high-quality, correctly mapped reads.
PacRAT is freely available, promoting wider adoption in the research community.