Transcript Slide 0

Bioinformatics
Bioinformatics
•
•
•
•
•
Sequence information
Mapping information
Phenotypic information
Literature
Prediction programs
-
Gene prediction
Promotor prediction
Functional prediction
Structural prediction
Variant annotation
http://www.ncbi.nlm.nih.gov/
Genome browsers
• ENSEMBL:
http://www.ensembl.org/index.html
• UCSC :
http://genome.ucsc.edu/
http://www.ensembl.org/index.html
Assembly converter
http://genome.ucsc.edu/
Assembly converter
https://decipher.sanger.ac.uk/
http://dgv.tcag.ca/dgv/app/home
Genomic variant analysis
• Genomic variants
- Mutation: literature, HGMD, gene specific
databases
- Polymorphism: dbSNP, EVS
- Prediction programs
http://www.ncbi.nlm.nih.gov/SNP/
http://evs.gs.washington.edu/EVS/
http://scholar.google.be
http://sift.jcvi.org/
CFTR: p.N1303K
CFTR: p.N1303K
Polyphen
http://genetics.bwh.harvard.edu/pph2/
Mutation Taster
http://www.mutationtaster.org/
But beware……!!!!!
There are many examples of known pathogenic variants
predicted to be benign and vice versa
Human Splicing Finder
http://www.umd.be/HSF/
Splice Site Prediction
http://www.fruitfly.org/seq_tools/splice.html
Splice finder programs
GeneSplicer
http://www.cbcb.umd.edu/software/
GeneSplicer/gene_spl.shtml
Netgene
http://www.cbs.dtu.dk/services/Net
Gene2/
NCBI
Ensembl
UCSC
http://www.ncbi.nlm.nih.gov/
http://www.ensemble.org/index.html
http://genome.ucsc.edu/
PolyPhen
SIFT
Mutation taster
Splice prediction
http://genetics.bwh.harvard.edu/pph2/
http://sift.jcvi.org/
http://www.mutationtaster.org/
http://www.umd.be/HSF/
http://www.fruitfly.org/seq_tools/splice.html
http://www.cbs.dtu.dk/services/NetGene2/
DECIPHER
https://decipher.sanger.ac.uk/