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Related Concept Videos

RNA-seq03:21

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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. 
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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.
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Related Experiment Video

Updated: Jun 4, 2026

A Rapid High-throughput Method for Mapping Ribonucleoproteins (RNPs) on Human pre-mRNA
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A Rapid High-throughput Method for Mapping Ribonucleoproteins (RNPs) on Human pre-mRNA

Published on: December 2, 2009

A Ruby API to query the Ensembl database for genomic features.

Francesco Strozzi1, Jan Aerts

  • 1Parco Tecnologico Padano, Lodi, Italy.

Bioinformatics (Oxford, England)
|February 1, 2011
PubMed
Summary
This summary is machine-generated.

A new Ruby API provides advanced querying of Ensembl genomic data, offering enhanced functionality and multi-species support. This tool simplifies access to genomic features for researchers.

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A Rapid High-throughput Method for Mapping Ribonucleoproteins (RNPs) on Human pre-mRNA
13:00

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Published on: December 2, 2009

Pattern-based Search of Epigenomic Data Using GeNemo
06:38

Pattern-based Search of Epigenomic Data Using GeNemo

Published on: October 8, 2017

Area of Science:

  • Bioinformatics
  • Genomics
  • Computational Biology

Background:

  • The Ensembl database offers access to genomic features via its Genome Browser.
  • Advanced data querying is currently supported through a Perl API.

Purpose of the Study:

  • To develop a comprehensive Ruby API for the Ensembl databases.
  • To provide enhanced functionality and simplify data access for researchers.

Main Methods:

  • The API utilizes the ActiveRecord pattern for most functionalities.
  • Introspection is employed to ensure release independence.
  • The library is distributed via the Rubygem system.

Main Results:

  • A full-featured Ruby API has been developed for Ensembl.
  • The API offers the same functionality as the Perl interface with additional features.
  • It supports access to different Ensembl database releases and multi-species queries.

Conclusions:

  • The Ruby API provides a powerful and flexible alternative for accessing Ensembl genomic data.
  • Its design facilitates easier integration and advanced querying for bioinformatics research.