bioinformatics. sequence information mapping information phenotypic information literature...
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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
Polyphenhttp://genetics.bwh.harvard.edu/pph2/
Mutation Tasterhttp://www.mutationtaster.org/
But beware……!!!!!
There are many examples of known pathogenic variants predicted to be benign and vice versa
Human Splicing Finderhttp://www.umd.be/HSF/
Splice Site Predictionhttp://www.fruitfly.org/seq_tools/splice.html
Splice finder programs
GeneSplicerhttp://www.cbcb.umd.edu/software/GeneSplicer/gene_spl.shtml
Netgenehttp://www.cbs.dtu.dk/services/NetGene2/
NCBI http://www.ncbi.nlm.nih.gov/Ensembl http://www.ensemble.org/index.htmlUCSC http://genome.ucsc.edu/
PolyPhen http://genetics.bwh.harvard.edu/pph2/SIFT http://sift.jcvi.org/Mutation taster http://www.mutationtaster.org/Splice prediction http://www.umd.be/HSF/
http://www.fruitfly.org/seq_tools/splice.htmlhttp://www.cbs.dtu.dk/services/NetGene2/
DECIPHER https://decipher.sanger.ac.uk/