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Related Concept Videos

RNA-seq03:21

RNA-seq

RNA sequencing, or RNA-Seq, is a high-throughput sequencing technology used to study the transcriptome of a cell. Transcriptomics helps to interpret the functional elements of a genome and identify the molecular constituents of an organism. Additionally, it also helps in understanding the development of an organism and the occurrence of diseases. 
Before the discovery of RNA-seq, microarray-based methods and Sanger sequencing were used for transcriptome analysis. However, while microarray-based...
Next-generation Sequencing03:00

Next-generation Sequencing

The first human genome sequencing project cost $2.7 billion and was declared complete in 2003, after 15 years of international cooperation and collaboration between several research teams and funding agencies. Today, with the advent of next-generation sequencing technologies, the cost and time of sequencing a human genome have dropped over 100 fold.
Next-Generation Sequencing Methods
Although all next-generation methods use different technologies, they all share a set of standard features.

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Related Experiment Video

Updated: May 31, 2026

Targeted Next-generation Sequencing and Bioinformatics Pipeline to Evaluate Genetic Determinants of Constitutional Disease
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Targeted Next-generation Sequencing and Bioinformatics Pipeline to Evaluate Genetic Determinants of Constitutional Disease

Published on: April 4, 2018

SeqGene: a comprehensive software solution for mining exome- and transcriptome- sequencing data.

Xutao Deng1

  • 1Bioinformatics Core Facility, Department of Molecular Medicine, Beckman Research Institute, City of Hope Medical Center, Duarte, CA 91010, USA. xutaodeng@gmail.com

BMC Bioinformatics
|July 1, 2011
PubMed
Summary
This summary is machine-generated.

SeqGene is a versatile new tool for analyzing massive sequencing data. It offers comprehensive features for mutation detection, gene expression analysis, and copy number variation detection, comparing favorably to existing methods.

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Cost-Efficient Transcriptomic-Based Drug Screening
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Last Updated: May 31, 2026

Targeted Next-generation Sequencing and Bioinformatics Pipeline to Evaluate Genetic Determinants of Constitutional Disease
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Published on: April 4, 2018

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Cost-Efficient Transcriptomic-Based Drug Screening

Published on: February 23, 2024

Area of Science:

  • Genomics
  • Bioinformatics
  • Computational Biology

Background:

  • Massively parallel sequencing projects necessitate advanced data mining tools.
  • Existing tools may lack comprehensive features for diverse analysis tasks.

Purpose of the Study:

  • To introduce SeqGene, a novel data mining tool for next-generation sequencing analysis.
  • To provide a comprehensive software package supporting a wide range of genomic analyses.

Main Methods:

  • SeqGene integrates mutation detection, annotation, and variant database (dbSNP, 1000 Genomes) integration.
  • It performs RNA-Seq expression quantification, copy number variation (CNV) analysis, and gene expression quantitative trait loci (eQTLs) detection.
  • Novel methods for SNP-expression association and genotype-controlled differential gene expression (DEGs) were developed.

Main Results:

  • SeqGene supports allele-specific expression (ASE) and differentially expressed genes (DEGs) identification.
  • Visualization tools for mutations and coverage are included.
  • Case studies demonstrate SeqGene's favorable comparison to existing methods.

Conclusions:

  • SeqGene is a general-purpose software package compatible with various sequencing platforms and computer systems.
  • It supports arbitrary genome assemblies and scales for projects of all sizes.
  • The software is available at http://seqgene.sourceforge.net.