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Related Concept Videos

Genome Annotation and Assembly03:36

Genome Annotation and Assembly

The genome refers to all of the genetic material in an organism. It can range from a few million base pairs in microbial cells to several billion base pairs in many eukaryotic organisms. Genome assembly refers to the process of taking the DNA sequencing data and putting it all back together in a correct order to create a close representation of the original genome. This is followed by the identification of functional elements on the newly assembled genome, a process called genome annotation.
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...
Assembly of Signaling Complexes01:30

Assembly of Signaling Complexes

Multiprotein signaling complexes are formed in a dynamic process involving protein-protein interactions at the cytoplasmic domain of transmembrane receptors or enzymatic and non-enzymatic proteins associated with the receptor. These complexes ensure the activation and propagation of intracellular signals that regulate cell functions.
Interaction domains in cell signaling
Interaction domains recognize exposed features of their binding partners containing post-translationally modified sequences,...
RACE - Rapid Amplification of cDNA Ends02:35

RACE - Rapid Amplification of cDNA Ends

Rapid Amplification of cDNA Ends, or RACE, is one of the most effective methods to obtain a full-length cDNA from an mRNA sequence between a known internal region to the unknown sequence at the 5’ or 3’ end. The unknown region is cloned in the cDNA by a gene-specific primer that binds the known end, and a hybrid primer that attaches a predefined anchor sequence to the unknown end of the cDNA. The sequence in between is amplified by PCR with an anchor primer and a gene-specific primer.
Since the...
Tagging and Fusion Proteins01:24

Tagging and Fusion Proteins

Proteins are involved in several cellular processes and biochemical reactions. Analyzing a specific protein of interest requires it to be isolated from the other proteins in the cell. This is achieved by overexpressing the specific gene in a suitable host to produce large quantities of the target protein. A tag or label is recombined with the gene to produce a fusion protein containing the target protein and the tag. The tags on these fusion proteins can then be used for easy detection and...
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 22, 2026

Comprehensive Workflow for the Genome-wide Identification and Expression Meta-analysis of the ATL E3 Ubiquitin Ligase Gene Family in Grapevine
10:40

Comprehensive Workflow for the Genome-wide Identification and Expression Meta-analysis of the ATL E3 Ubiquitin Ligase Gene Family in Grapevine

Published on: December 22, 2017

Global assembly of expressed sequence tags.

Foo Cheung1

  • 1Center for Human Immunology, Autoimmunity, and Inflammation, National Institute of Health, Bethesda, MD, USA. foo.cheung@nih.gov

Methods in Molecular Biology (Clifton, N.J.)
|May 17, 2012
PubMed
Summary

This study details a method for constructing Expressed Sequence Tag (EST) assemblies using diverse sequencing technologies. The approach integrates data from 454, Sanger, and Illumina (Solexa) sequencing for comprehensive transcript analysis.

Area of Science:

  • Bioinformatics
  • Genomics
  • Molecular Biology

Background:

  • Expressed Sequence Tag (EST) assemblies are crucial for gene discovery and analysis.
  • Existing EST assembly protocols, like TIGR Gene Indices, provide a foundation for new methods.
  • Integrating diverse sequencing technologies presents challenges and opportunities for transcriptomics.

Purpose of the Study:

  • To describe a novel method for constructing EST assemblies.
  • To incorporate reads from 454 pyrosequencing, Sanger sequencing, and Illumina (Solexa) sequencing technologies.
  • To outline strategies for handling different read lengths and types in a unified assembly process.

Main Methods:

  • Utilizing reads from 454, Sanger, and Illumina (Solexa) sequencing as input.

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Multiplexed Analysis of Retinal Gene Expression and Chromatin Accessibility Using scRNA-Seq and scATAC-Seq
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Multiplexed Analysis of Retinal Gene Expression and Chromatin Accessibility Using scRNA-Seq and scATAC-Seq

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Droplet Barcoding-Based Single Cell Transcriptomics of Adult Mammalian Tissues
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Droplet Barcoding-Based Single Cell Transcriptomics of Adult Mammalian Tissues

Published on: January 10, 2019

Related Experiment Videos

Last Updated: May 22, 2026

Comprehensive Workflow for the Genome-wide Identification and Expression Meta-analysis of the ATL E3 Ubiquitin Ligase Gene Family in Grapevine
10:40

Comprehensive Workflow for the Genome-wide Identification and Expression Meta-analysis of the ATL E3 Ubiquitin Ligase Gene Family in Grapevine

Published on: December 22, 2017

Multiplexed Analysis of Retinal Gene Expression and Chromatin Accessibility Using scRNA-Seq and scATAC-Seq
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Multiplexed Analysis of Retinal Gene Expression and Chromatin Accessibility Using scRNA-Seq and scATAC-Seq

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Droplet Barcoding-Based Single Cell Transcriptomics of Adult Mammalian Tissues
10:12

Droplet Barcoding-Based Single Cell Transcriptomics of Adult Mammalian Tissues

Published on: January 10, 2019

  • Incorporating internally generated EST reads and publicly available data from dbEST and GenBank.
  • Applying de novo assembly or align-then-assemble approaches for shorter reads (Solexa).

    • Main Results:

    • Demonstrated a consistent EST assembly method adaptable to various sequencing inputs.
    • Showcased strategies for integrating short reads (Solexa) with longer reads (454, Sanger).
    • Highlighted the flexibility to include or exclude virtual transcripts based on project requirements.

    Conclusions:

    • The described method enables robust EST assembly by integrating multiple sequencing platforms.
    • Specialized handling of shorter reads is necessary for successful global EST assembly.
    • This approach enhances the comprehensive analysis of transcriptomes from diverse data sources.