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Related Concept Videos

Maxam-Gilbert Sequencing01:05

Maxam-Gilbert Sequencing

In the same year as the discovery of the Sanger sequencing method, another group of scientists, Allan Maxam and Walter Gilbert, demonstrated their chemical-cleavage method for DNA sequencing. The Maxam-Gilbert method relies on using different chemicals that can cleave the DNA sequence at specific sites, the separation of resulting DNA fragments of variable size using electrophoresis, and deciphering the DNA sequence from the resulting gel bands.
Challenges of the Maxam-Gilbert Method
The...
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.
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.
Sanger Sequencing01:57

Sanger Sequencing

DNA sequencing is a fundamental technique that is routinely used in the biological sciences. This method can be applied to a range of questions at different scales - from the sequencing of a cloned DNA fragment or the study of a mutation in a gene up to whole-genome sequencing. However, despite the widespread use of sequencing today, it was not until 1977 that Fredrick Sanger and his collaborators developed the chain-termination method to decode DNA sequences. It relies on the separation of a...
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...
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...

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Related Experiment Video

Updated: Jun 4, 2026

Primer Extension Capture: Targeted Sequence Retrieval from Heavily Degraded DNA Sources
15:28

Primer Extension Capture: Targeted Sequence Retrieval from Heavily Degraded DNA Sources

Published on: September 3, 2009

GeneReporter--sequence-based document retrieval and annotation.

Annekathrin Bartsch1, Boyke Bunk, Isam Haddad

  • 1Institute for Microbiology, Technische Universität Braunschweig, Braunschweig, Germany.

Bioinformatics (Oxford, England)
|February 12, 2011
PubMed
Summary

GeneReporter is a web tool that aids in genome annotation and literature retrieval for protein-coding sequences. It provides functional data and PubMed references by analyzing homologous sequences.

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Last Updated: Jun 4, 2026

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Area of Science:

  • Bioinformatics
  • Genomics
  • Molecular Biology

Background:

  • Manual genome annotation and document retrieval are crucial for understanding protein-coding sequences.
  • Accessing comprehensive functional information and relevant literature for genes can be challenging.

Purpose of the Study:

  • To introduce GeneReporter, a web tool designed to streamline the process of obtaining functional information and literature for protein-coding sequences.
  • To support researchers in manual genome annotation and efficient document retrieval.

Main Methods:

  • GeneReporter utilizes UniProt entries of homologous sequences to extract query words for PubMed reference detection.
  • It integrates data from protein families, domains, cofactors, structure, function, cellular localization, and metabolic contribution.
  • The tool leverages SOAP-based web services from the European Bioinformatics Institute (EBI) and the National Center for Biotechnology Information (NCBI).

Main Results:

  • GeneReporter provides a centralized platform for accessing diverse functional data related to protein-coding sequences.
  • It facilitates the identification of relevant scientific literature through automated PubMed reference retrieval.
  • The tool enhances the efficiency of genome annotation by consolidating essential information.

Conclusions:

  • GeneReporter serves as a valuable resource for researchers involved in genomics and molecular biology.
  • The web tool simplifies the discovery of functional insights and scientific literature for protein-coding sequences.
  • Its integration with major bioinformatics databases enhances its utility for biological research.