Learn to use the tools at DCODE.org, 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 DCODE.org 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 will 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


This tutorial is a part of the tutorial group Alignment and comparison resources. You might find the other tutorials in the group interesting:

ClustalW2: Performs multiple sequence alignments

BLAST: Basic Local Alignment and Search Tool

FASTA: FASTA sequence algorithm

Entrez Gene: NCBI's Entrez tool for gene-centric information

Primer3: Pick primers from a DNA sequence.

VISTA: Tools for Comparative Genomics

RefSeq: Provides molecular sequence records to help locate gene and protein data.


Algorithms and Analysis : This category contains various tools that may help perform analysis of different genomics data types. This may include sequence alignment, large-scale or complex queries, motif finding, or comparative assessments.

NCBI : This category includes resources maintained at the National Center for Biotechnology Information (NCBI).


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