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