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:
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).
New Online Tutorials for NCBI resources BioSystems and DCODE: Comprehensive tutorials on the publicly available NCBI resources BioSystems and DCODE enable researchers to quickly and effectively use these invaluable resources. Seattle, WA (PRWEB) February 23, 2010...
(re)Funding Databases II: So, I wrote about defunding resources and briefly mentioned a paper in Database about funding (or 're'funding) databases and resources. I'd like to discuss this a bit further. The paper, by Chandras et...
Recent BioMed Central research articles citing this resource
El Taghdouini Adil et al., In vitro reversion of activated primary human hepatic stellate cells. Fibrogenesis Tissue Repair (2015) doi:10.1186/s13069-015-0031-z
Gutiérrez Verónica et al., First complete mitochondrial genome of the South American annual fish Austrolebias charrua (Cyprinodontiformes: Rivulidae): peculiar features among cyprinodontiforms mitogenomes Comparative and evolutionary genomics. BMC Genomics (2015) doi:10.1186/s12864-015-2090-3
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