EDUCATION
How your DNA folds.
Interview with Dr. Job Dekker, professor at the University of Massachusetts Medical School
Useful epigenetics, molecular biology and bioinformatic tools:
WashU Epigenome Browser: http://epigenomegateway.wustl.edu/
UCSC Genome Browser: http://genome.ucsc.edu/
http://source-search.princeton.edu/cgi-bin/source/sourceSearch (prokaryote and eukaryote genes)
http://www.ebi.ac.uk/gxa/home (expression atlas for many eukaryotes)
http://ist.medisapiens.com/#broad-healthy (expression in normal and malignant human tissues)
http://igc.otago.ac.nz/home.html (imprinted genes catalogue
NIH genetic sequence database: http://www.ncbi.nlm.nih.gov/genbank/
Annotation of alternative RNA and gene isoforms & tissue-specific expression:
http://www.ensembl.org/index.html
http://genatlas.medecine.univ-paris5.fr/
NCBI Gene Expression Omnibus: http://www.ncbi.nlm.nih.gov/geoprofiles/
General design of DNA primers: http://www.ncbi.nlm.nih.gov/tools/primer-blast/
GEO datasets for functional genomics: http://www.ncbi.nlm.nih.gov/geo/
DAVID functional annotation: http://david.abcc.ncifcrf.gov/
GeneCards (now has a fee for GO analysis): http://www.genecards.org/
GREAT functional annotation that also considers genes that are nearby even if they are not the
closest gene to DNA regions of interest: http://bejerano.stanford.edu/great/public/html/index.php
Transcription factor (TF) binding sites: http://www.gene-regulation.com/pub/databases.html
In UCSC Genome Browser, rodent/human conserved TFBS, and ChIP-seq observed TFBS: http://genome.ucsc.edu
CTCF searchable database: CTCFBSDB http://insulatordb.uthsc.edu
Enhancers that were in vivo tested (and negative tested candidates): http://enhancer.lbl.gov/
CisFinder, identification of DNA overrepresented motifs: http://lgsun.grc.nia.nih.gov/CisFinder/
CpG Island Searcher: http://www.uscnorris.com/cpgislands2/cpg.aspx
Finding restriction enzymes for a given recognition site or sequence:
https://www.neb.com/tools-and-resources/interactive-tools/enzyme-finder
http://nc2.neb.com/NEBcutter2/
Effects of CpG methylation on restriction enzyme cleavage: https://www.neb.com/tools-andresources/usage-guidelines/effects-of-cpg-methylation-on-restriction-enzyme-cleavage
Comparing cis elements between genes or within a conserved sequence:
http://genometrafac.cchmc.org/genome-trafac/index.jsp
Tm calculator: http://tmcalculator.neb.com/#!/
miRBase, A searchable database of published miRNA sequences and annotation:
http://www.mirbase.org/
TarBase, The largest manually curated target database, indexing more than 65,000 miRNA-gene
interactions: http://diana.imis.athena-innovation.gr/DianaTools/index.php?r=tarbase/index
TF binding and expression including diverse ncRNA genes: http://deepbase.sysu.edu.cn/chipbase/
