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OpenHelix Comparative Genomics Developments, a collection of powerful comparative genomics tools

Tutorial and training materials by OpenHelix

Learn to use the tools at, which are a collection of powerful comparative genomics resources. DCODE tools enable the user to browse several vertebrate genomes and compare them to identify ECRs (or evolutionary conserved regions). These regions, conserved through time often perform important regulatory functions. DCODE tools not only enable the user to identify ECRs but also to perform pairwise and multiple sequence alignments to create conservation profiles and phylogenetic tress. DCODE resources also have the capability to identify proximal and distant regulatory elements and conserved transcription factor binding sites. This tutorial will give you an introduction and overview of several of the tools available at and soon you will be searching your genomes and sequences of interest for regulatory elements and increasing your understanding of the mechanisms of gene regulation hidden there.

You'll learn:

  • how to conduct whole genome alignments and identify ECRs
  • how to create interactive conservation profiles and phylogenetic tress
  • how to identify proximal and distant regulatory elements in desired sequences
  • identify conserved transcription factor binding sites


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Recent BioMed Central research articles citing this resource

Teng Shaolei et al., Genome-wide prediction and analysis of human tissue-selective genes using microarray expression data Proceedings of the 2011 International Conference on Bioinformatics and Computational Biology (BIOCOMP"11) The 2011 International Conference on Bioinformatics and Computational Biology (BIOCOMP"11). BMC Medical Genomics (2013) doi:10.1186/1755-8794-6-S1-S10

Peña-Chilet Maria et al., Genetic variants in PARP1 (rs3219090) and IRF4 (rs12203592) genes associated with melanoma susceptibility in a Spanish population Genetics, genomics and epigenetics. BMC Cancer (2013) doi:10.1186/1471-2407-13-160

Yang Ninghan et al., Genetic basis for phenotypic differences between different Toxoplasma gondii type I strains Eukaryote microbial genomics. BMC Genomics (2013) doi:10.1186/1471-2164-14-467

Sgadò Paola et al., The atypical homeoprotein Pbx1a participates in the axonal pathfinding of mesencephalic dopaminergic neurons. Neural Development (2012) doi:10.1186/1749-8104-7-24

Keskin Havva et al., Complex effects of flavopiridol on the expression of primary response genes. Cell Division (2012) doi:10.1186/1747-1028-7-11

More about the resource:

DCODE, which stands for Comparative Genomics Developments was established in 2003 as a part of NCBI. The main goal of DCODE is to provide scientists with centralized access to a variety of tools that allow for comparative sequence analysis therefore aiding in the understanding of the vast array of gene regulatory networks that exist throughout vertebrate genomes.

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The materials and slides offered can not be resold or used for profit purposes. Reproduction, distribution and/or use is strictly limited to instructional purposes only and can not be used for for monetary gain or wide distribution.
Copyright 2009, OpenHelix, LLC.

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