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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