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Recommended Resources

Below is a list of web resources you may find useful to refer to. Please take a look at some of the introductory pages e.g. FAQ’s, tutorial pages to give you an idea of the terminology, and the appropriate context in which some of tools and technologies are used in the clinical bioinformatician’s workflow. Please select this link to launch a pdf version for you to download of this resources list.

Nomenclature

Accession number guide http://www.ncbi.nlm.nih.gov/Sequin/acc.html
HGNC http://www.genenames.org/
HGVS http://www.hgvs.org/
LRG http://www.lrg-sequence.org/
Genome Reference Consortium http://www.ncbi.nlm.nih.gov/projects/genome/assembly/grc/human/index.shtml
Mutalyzer https://mutalyzer.nl/

Sequence Databases

INSDC www.insdc.org/
EBI www.ebi.ac.uk/ena/
DDBJ www.ddbj.nig.ac.jp/
GenBank www.ncbi.nlm.nih.gov/genbank
RefSeq www.ncbi.nlm.nih.gov/RefSeq/
RefSeqGene www.ncbi.nlm.nih.gov/refseq/rsg/
UniProt www.ebi.ac.uk/uniprot/
EBI training http://www.ebi.ac.uk/training/online/

Genome Browsers

Ensembl Genome Browser www.ensembl.org/index.html
UCSC Genome Browser www.genome.ucsc.edu/cgi-bin/hgGateway

Genome Projects

Human Genome Project www.ornl.gov/sci/techresources/Human_Genome/home.shtml
Human Variome Project www.humanvariomeproject.org/
1000 Genomes Project www.1000genomes.org/
Mouse Genome Informatics www.informatics.jax.org/
100000 Genomes Project http://www.genomicsengland.co.uk/
UK 10000 genomes project http://www.uk10k.org/
Personal genome project http://www.personalgenomes.org/

Variation Databases

dbSNP www.ncbi.nlm.nih.gov/projects/SNP/
DGV http://dgv.tcag.ca/dgv/app/home

Phenotype Databases

OMIM www.ncbi.nlm.nih.gov/omim
GEN2PHEN www.gen2phen.org/
European Genome/Phenome archive https://www.ebi.ac.uk/ega/home

Variant Databases

HGVS LSDB listing www.hgvs.org/dblist/glsdb.html
InSiGHT www.insight-group.org/
Ecaruca http://umcecaruca01.extern.umcn.nl:8080/ecaruca/
Decipher http://decipher.sanger.ac.uk/
HGMD www.hgmd.cf.ac.uk/ac/index.php
Unique http://www.rarechromo.org/html/home.asp
dbVar http://www.ncbi.nlm.nih.gov/dbvar/
ISCA https://www.iscaconsortium.org/
LOVD www.lovd.nl/2.0/
Exome Aggregation Consortium http://exac.broadinstitute.org/
ClinVar http://www.ncbi.nlm.nih.gov/clinvar/

Sequence Alignment

Sequence Tools www.ebi.ac.uk/Tools/
Sequence Similarity www.ebi.ac.uk/Tools/sss/
Sequence Alignment www.ebi.ac.uk/Tools/msa/

Variant Interpretation

ALIGN-GVGD www.agvgd.iarc.fr/agvgd_input.php
PolyPhen-2 www.genetics.bwh.harvard.edu/pph2/
SIFT www.sift.jcvi.org/
Alamut www.interactive-biosoftware.com/alamut.html
Missense tools http://www.ngrl.org.uk/Manchester/page/missense-prediction-tools
Variant effect predictor http://www.ensembl.org/info/docs/tools/vep/index.html

Literature Resources

PubMed www.ncbi.nlm.nih.gov/pubmed/
Google Scholar www.scholar.google.co.uk

Ontologies

Gene Ontology www.geneontology.org/
HPO http://human-phenotype-ontology.org/

Rare Disease Registries

Orphanet http://www.orpha.net/consor/cgi-bin/index.php
Rare diseases https://www.rarediseases.org

Patient Fora

Patients like me http://www.patientslikeme.com/

Genetic disease charities

Genetic Alliance http://www.geneticalliance.org.uk/
Jeans for genes day http://www.jeansforgenesday.org/aboutjeansforgenesday

UK Genetic Testing Network

UK Genetic Testing Network http://ukgtn.nhs.uk/

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This article is from the free online course:

Clinical Bioinformatics: Unlocking Genomics in Healthcare

The University of Manchester