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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