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/