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Updated: Jul 5, 2026

Informatic Analysis of Sequence Data from Batch Yeast 2-Hybrid Screens

Informatic Analysis of Sequence Data from Batch Yeast 2-Hybrid Screens

Published on: June 28, 2018

A scaffold analysis tool using mate-pair information in genome sequencing.

Pan-Gyu Kim¹, Hwan-Gue Cho, Kiejung Park

¹SmallSoft Co., Ltd., Jang-Dong 59-5, Yusung-Gu, Daejeon 305-343, South Korea.

Journal of Biomedicine & Biotechnology

|April 17, 2008

Summary

This summary is machine-generated.

ConPath is a new Windows program that analyzes genome assemblies. It orders and orients sequence contigs using mate-pair information to build accurate genome scaffolds, improving assembly verification.

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High-throughput Identification of Gene Regulatory Sequences Using Next-generation Sequencing of Circular Chromosome Conformation Capture (4C-seq)

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A Pathway Association Study Tool for GWAS Analyses of Metabolic Pathway Information

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Published on: July 1, 2020

Area of Science:

Genomics
Bioinformatics
Computational Biology

Background:

Genome assembly is a critical step in understanding genomic sequences.
Accurate ordering and orientation of sequence contigs are essential for reliable genome assembly.
Existing tools may have limitations in handling complex assembly data and identifying errors.

Purpose of the Study:

To introduce ConPath, a novel Windows-based scaffold analyzer.
To present an algorithm for constructing genome scaffolds by ordering and orienting sequence contigs.
To provide tools for verifying genome assembly accuracy and identifying erroneous contigs.

Main Methods:

Developed a scaffold analyzer program, ConPath, for Windows operating systems.
Implemented an algorithm that builds directed graphs from contig link information and traverses them to find the longest acyclic graphs.
Utilized mate-pair information from fixed-sized libraries to determine contig orientations and estimate gap sizes.
Incorporated validation steps to report assembly errors based on orientations and gap sizes.

Main Results:

ConPath successfully constructs scaffolds by ordering and orienting sequence contigs.
The program accurately determines relative orientations and estimates gap sizes between contigs.
ConPath identified erroneous contigs in over 10 microbial genome projects, including *Mannheimia succiniciproducens* and *Vibrio vulnificus*.
The software provides detailed viewers for investigating contigs and scaffolds.

Conclusions:

ConPath is an effective tool for scaffold analysis and genome assembly verification.
The program aids in identifying and correcting assembly errors, leading to more accurate genome sequences.
ConPath offers valuable features for detailed investigation of genome assembly components.