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/