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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...
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.
Cis-regulatory Sequences02:02

Cis-regulatory Sequences

Cis-regulatory sequences are short fragments of non-coding DNA that are present on the same chromosomes as the genes that they regulate. These fragments serve as binding sites for transcriptional regulators, proteins that are responsible for controlling gene transcription and differential gene expression across cell types in eukaryotes. Cis-regulatory sequences can be close to the gene of interest or thousands of bases away in the DNA sequence; however, those sequences that are further away are...
Cis-regulatory Sequences02:02

Cis-regulatory Sequences

Cis-regulatory sequences are short fragments of non-coding DNA that are present on the same chromosomes as the genes that they regulate. These fragments serve as binding sites for transcriptional regulators, proteins that are responsible for controlling gene transcription and differential gene expression across cell types in eukaryotes. Cis-regulatory sequences can be close to the gene of interest or thousands of bases away in the DNA sequence; however, those sequences that are further away are...
Multi-species Conserved Sequences02:51

Multi-species Conserved Sequences

Next-generation sequencing technologies have created large genomic databases of a variety of animals and plants. Ever since the human genome project was completed, scientists studied the genome of primates, mammals, and other phylogenetically distant living beings. Such large-scale  studies have provided new insights into the evolutionary relationship between organisms.
Although the genome of each species varies greatly from each other, a few sequences are highly conserved. Such conserved DNA...
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...

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Related Experiment Video

Updated: Jun 19, 2026

Novel Sequence Discovery by Subtractive Genomics
09:40

Novel Sequence Discovery by Subtractive Genomics

Published on: January 25, 2019

Non-redundant patent sequence databases with value-added annotations at two levels.

Weizhong Li1, Hamish McWilliam, Ana Richart de la Torre

  • 1European Bioinformatics Institute, EMBL Outstation, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK.

Nucleic Acids Research
|November 4, 2009
PubMed
Summary
This summary is machine-generated.

The European Bioinformatics Institute created non-redundant patent sequence databases to address challenges in searching and analyzing patent data. These databases offer enhanced annotations for improved tracking and cross-referencing of scientific and intellectual property information.

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

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The ITS2 Database
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The ITS2 Database

Published on: March 12, 2012

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Last Updated: Jun 19, 2026

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Published on: January 25, 2019

Targeted Next-generation Sequencing and Bioinformatics Pipeline to Evaluate Genetic Determinants of Constitutional Disease
09:34

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

Published on: April 4, 2018

The ITS2 Database
16:17

The ITS2 Database

Published on: March 12, 2012

Area of Science:

  • Bioinformatics
  • Intellectual Property Law
  • Sequence Analysis

Background:

  • Public access to patent data, including sequences, is provided by the European Bioinformatics Institute (EMBL-EBI).
  • Redundancy and incomplete annotations in patent sequence data pose challenges for scientific and intellectual-property communities.
  • Existing patent sequence databases lack value-added annotations crucial for effective data analysis.

Purpose of the Study:

  • To develop a collection of non-redundant patent sequence databases.
  • To enhance the quality and usability of patent sequence data for researchers and patent professionals.
  • To facilitate better tracking and cross-referencing of patent-related biological information.

Main Methods:

  • Creation of non-redundant databases using sequence MD5 checksums for clustering.
  • Development of two-level clustering: Level-1 for identical sequences, Level-2 for patent family grouping.
  • Inclusion of value-added annotations such as publication number corrections and earliest publication dates.

Main Results:

  • A collection of non-redundant patent sequence databases covering EMBL-Bank nucleotides and patent protein classes was established.
  • Sequence data was clustered at two levels, ensuring 100% identity within Level-1 clusters and grouping by patent family in Level-2.
  • Value-added annotations significantly improved data quality, enabling enhanced tracking and cross-referencing.

Conclusions:

  • The new non-redundant patent sequence databases provide a valuable resource for bioinformatics and intellectual property research.
  • Enhanced data quality and accessibility facilitate more efficient analysis of patent-related sequence information.
  • These databases improve the ability to track and cross-reference inventions and their associated biological data across multiple patent filings.