BioSilico3
Diego Forero, MD, PhD
Personal Website
BioSilicoList
A comprehensive list of available in silico tools for genetics and genomics
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Human genetics/genomics
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*Databases
dbSNP http://www.ncbi.nlm.nih.gov/projects/SNP/
HapMap http://www.hapmap.org/cgi-perl/gbrowse/hapmap27_B36/
Database of Genomic Variants http://projects.tcag.ca/variation/
HuGe Navigator http://www.hugenavigator.net/
Human Gene Mutation Database http://www.hgmd.cf.ac.uk/ac/index.php
HUGO Gene Nomenclature Committee http://www.genenames.org/
HGVbaseG2P http://www.hgvbaseg2p.org/index
SNPedia http://www.snpedia.com/index.php/SNPedia
HGDP-CEPH Human Genome Diversity Cell Line Panel http://www.cephb.fr/en/hgdp/diversity.php/
DNA Polymorphism Discovery Resource http://www.genome.gov/10001552 Coriell
Mexican Genome Diversity Project http://diversity.inmegen.gob.mx
Online Encyclopedia for Genetic Epidemiology studies http://www.oege.org/
ALFRED http://alfred.med.yale.edu/alfred/index.asp
Singapore genome variation project http://www.nus-cme.org.sg:8080/cgi-bin/gbrowse/sgvp/
List of Individual Human Genomes Sequenced http://sites.google.com/site/neurocienciaspanam/genomes
Locus Specific Mutation Databases http://www.genomic.unimelb.edu.au/mdi/dblist/glsdb.html
Frequency of Inherited Disorders Database http://archive.uwcm.ac.uk/uwcm/mg/fidd/search.html
EvidenceProject https://slep.unc.edu/evidence
AlzGene http://www.alzforum.org/res/com/gen/alzgene/default.asp
PDGene http://www.pdgene.org/
SZGene http://www.schizophreniaforum.org/res/sczgene/default.asp
Hereditary Hearing Loss Homepage http://webh01.ua.ac.be/hhh/
Parkinson's disease Mutation Database http://grenada.lumc.nl/LOVD2/TPI/home.php
Mutation Database for Parkinson's Disease http://datam.i2r.a-star.edu.sg/mdpd/index.php
Alzheimer Disease & Frontotemporal Dementia Mutation Database http://www.molgen.ua.ac.be/ADMutations/
Inherited Peripheral Neuropathies Mutation Database http://www.molgen.ua.ac.be/CMTMutations/Home/IPN.cfm
Schizophrenia Gene Resource SZGR http://bioinfo.vipbg.vcu.edu:8080/SZGR/index.jsp
GeneCards Disease Genes http://www.genecards.org/cgi-bin/listdiseasecards.pl?type=full
List of X-linked Mental Retardation Genes http://xlmr.interfree.it/Genes.pdf
Ethanol-Related Gene Resource http://bioinfo.vipbg.vcu.edu/ERGR/
CarpeDB http://www.carpedb.ua.edu/
NeuroPsyGenMut http://sites.google.com/site/compgensite/neuropsygenmut
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*Servers/Programs
PLINK http://pngu.mgh.harvard.edu/~purcell/plink/
Haploview http://www.broad.mit.edu/mpg/haploview/
GOLD http://www.sph.umich.edu/csg/abecasis/GOLD/download/
SNPstats http://bioinfo.iconcologia.net/index.php?module=Snpstats
Structure http://pritch.bsd.uchicago.edu/software.html
Q-VALUE http://genomics.princeton.edu/storeylab/qvalue/
Genetic Power Calculator http://pngu.mgh.harvard.edu/~purcell/gpc/
CLUMP http://www.smd.qmul.ac.uk/statgen/dcurtis/software.html
EasyLinkage http://genetik.charite.de/hoffmann/easyLINKAGE/index.html
Catmap http://cran.r-project.org/web/packages/catmap/index.html
Mutation Checker http://mutation.sanbi.ac.za/checker
Variant Name Mapper http://www.hugenavigator.net/HuGENavigator/startPageMapper.do
PGA http://dceg.cancer.gov/bb/tools/pga
Power/Sample Size Calculator http://www.stat.ubc.ca/~rollin/stats/ssize/b2.html
Power Calculator http://homepage.stat.uiowa.edu/~rlenth/Power/
CaTS -- Power Calculator for Two Stage Association Studies http://www.sph.umich.edu/csg/abecasis/cats/index.html
Power Calculator http://www.cs.uiowa.edu/~rlenth/Power/
GENESTAT http://www.genestat.org/
Statistics tests-Guide http://gettinggeneticsdone.blogspot.com/2009/03/whats-right-analysis-for-this-data.html
Rgenetics http://rgenetics.org/
CLUMPHAP http://www.smd.qmul.ac.uk/statgen/software/dcurtis/clumphap1_0.zip
SNPSpD http://gump.qimr.edu.au/general/daleN/SNPSpD/
WGAViewer http://people.genome.duke.edu/~dg48/WGAViewer/
GWAS GUI http://www.sph.umich.edu/csg/weich/browser/
GoldSurfer2 http://www.well.ox.ac.uk/gs2/
Sumstat http://linkage.rockefeller.edu/ott/sumstat.html
HWE and tests of association http://ihg2.helmholtz-muenchen.de/cgi-bin/hw/hwa1.pl
genetic map position of SNPs http://actin.ucd.ie/cgi-bin/rs2cm.cgi
BayesMeta http://homepages.lshtm.ac.uk/~encdpnew/
Metal http://www.sph.umich.edu/csg/abecasis/Metal/index.html
MANTEL http://www.broadinstitute.org/~debakker/mantel.html
HEGESMA http://biomath.med.uth.gr/files/HEGESMA_v2.0.exe
GSMA http://www.kcl.ac.uk/schools/medicine/depts/memoge/research/epidemiology/gsma/download.html
SNPinfo-Candidate Gene SNP Selection http://manticore.niehs.nih.gov/selegene.htm
SNPinfo-TAG SNP Selection http://manticore.niehs.nih.gov/snptag.htm
GLIDERS http://mather.well.ox.ac.uk/GLIDERS/
Human genetic maps-marshfield clinic http://research.marshfieldclinic.org/genetics/GeneticResearch/compMaps.asp
Linkdatagen http://bioinf.wehi.edu.au/software/linkdatagen/index.html
IGG3 http://bioinfo.hku.hk:13080/iggweb/
CRAN-Statistical Genetics http://cran.r-project.org/web/views/Genetics.html
LD-Plus https://chgr.mc.vanderbilt.edu/ldplus/create/setparams
QuickCalcs http://www.graphpad.com/quickcalcs/
MetaP http://people.genome.duke.edu/~dg48/metap.php
MQLS http://www.sph.umich.edu/csg/liang/MQLS/
AutoSNPa http://dna.leeds.ac.uk/autosnpa/
EXCLUDEAR http://leedsdna.info/Archived%20pages%20and%20files/science/Autozygosity/spreadsheets.htm
SNPsetter http://dna.leeds.ac.uk/snpsetter/
IBDfinder http://dna.leeds.ac.uk/ibdfinder/
SNPannotator http://dna.leeds.ac.uk/snpannotator/
HomozygosityMapper http://www.homozygositymapper.org/
Madeline 2.0 PDE http://eyegene.ophthy.med.umich.edu/madeline/webservice.php
MimMiner http://www.cmbi.ru.nl/MimMiner/cgi-bin/main.pl
PhenExplorer http://www.human-phenotype-ontology.org/PhenExplorer/PhenExplorer.html
My Family Health Portrait https://familyhistory.hhs.gov/fhh-web/home.action
Phenomizer http://compbio.charite.de/Phenomizer/Phenomizer.html
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*Tools for Analysis of Functional SNPs/Variants:
F-SNP http://compbio.cs.queensu.ca/F-SNP/
SNPseek http://snp.wustl.edu/cgi-bin/SNPseek/index.cgi
Patrocles http://www.patrocles.org/MyPatrocles.php
PupaSuite http://pupasuite.bioinfo.cipf.es/
PolyPhen http://genetics.bwh.harvard.edu/pph/
SNPs3D http://www.snps3d.org/
SNP@Ethnos http://variome.kobic.re.kr/SNPatETHNIC/Wiki.jsp?page=EthnicallyVariantSNP
PANTHER Coding SNP Analysis Tool http://www.pantherdb.org/tools/csnpScoreForm.jsp
topoSNP http://gila.bioengr.uic.edu/snp/toposnp/
SNPeffect http://snpeffect.vib.be/
LS-SNP http://modbase.compbio.ucsf.edu/LS-SNP//Queries.html
PMut http://mmb2.pcb.ub.es:8080/PMut/
SNAP http://cubic.bioc.columbia.edu/services/SNAP/submit.html
StSNP http://glinka.bio.neu.edu/StSNP
dbSMR http://miracle.igib.res.in/polyreg/
PolyDoms http://polydoms.cchmc.org/polydoms/
Functional SNP Database http://bioinfo.hku.hk:13080/funcsnpweb/
MedRefSNP http://medclue.com/medrefsnp/
SNP2NMD Database http://variome.kobic.re.kr/SNP2NMD/Wiki.jsp?page=SearchInterface
SNPinfo-Functional SNP Selection Based on GWAS http://manticore.niehs.nih.gov/selegwas.htm
SNPinfo-Functional SNP Prediction http://manticore.niehs.nih.gov/snpfunc.htm
F-nsSNP-Syn-Gen http://sites.google.com/site/compgensite/f-nssnp-syn-gen
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*Tools for Design/Analysis of Genotyping Experiments
BatchPrimer3 http://probes.pw.usda.gov/cgi-bin/batchprimer3/batchprimer3.cgi
Tetra-primer ARMS-PCR design http://cedar.genetics.soton.ac.uk/public_html/primer1.html
WASP http://bioinfo.biotec.or.th/WASP
PIRA http://cedar.genetics.soton.ac.uk/public_html/primer2.html
UCSC In-Silico PCR http://genome.ucsc.edu/cgi-bin/hgPcr?org=Human&db=hg
SNPbox http://www.snpbox.org/
MethPrimer http://www.urogene.org/methprimer/index1.html
MultiPLX 2.0 http://bioinfo.ut.ee/multiplx/
MultiPrimer http://edith.cse.nsysu.edu.tw/new/software/MultiPrimer.htm
MuPlex http://genomics14.bu.edu:8080/MuPlex/MuPlex.html
FastPCR http://www.biocenter.helsinki.fi/bi/Programs/download.htm
AutoDimer http://yellow.nist.gov:8444/dnaAnalysis/primerToolsPage.do
SNP-Flankplus http://bio.kuas.edu.tw/snp-flankplus/snpin.jsp
EasyExonPrimer http://129.43.22.27/~primer/EasyExonPrimer.html
Multiplex Manager http://www.multiplexmanager.com/
MutScreener http://bioinfo.bsd.uchicago.edu/MutScreener.html
novoSNP http://www.molgen.ua.ac.be/bioinfo/novosnp/
VarDetect http://www4a.biotec.or.th/GI/tools/vardetect
GeneScreen http://dna.leeds.ac.uk/genescreen/
QSVanalyser http://dna.leeds.ac.uk/qsv/
Prim-SNPing http://bio.kuas.edu.tw/prim-snping/
InSNP http://www.mucosa.de/insnp/
SNPdetector ftp://ftp1.nci.nih.gov/pub/SNPdetector/
SGCaller http://www.mucosa.de/sgcaller/
SNP Affycomp http://rafalab.jhsph.edu/snpaffycomp/
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*Regulatory factors/regions
miRBase http://microrna.sanger.ac.uk/sequences/
Jaspar http://jaspar.cgb.ki.se/
mfold http://frontend.bioinfo.rpi.edu/applications/mfold/cgi-bin/rna-form1.cgi
RNAfold http://rna.tbi.univie.ac.at/cgi-bin/RNAfold.cgi
TargetCombo http://www.diana.pcbi.upenn.edu/cgi-bin/TargetCombo.cgi
human microRNA disease database http://202.38.126.151/hmdd/html/test2.html
MAPPER http://snpper.chip.org/mapper/mapper-main
RNAhybrid http://bibiserv.techfak.uni-bielefeld.de/rnahybrid/
TargetScan http://www.targetscan.org/
MiRanda http://www.microrna.org/microrna/getGeneForm.do
PicTar http://pictar.bio.nyu.edu/
NRED http://jsm-research.imb.uq.edu.au/NRED
TarBase http://diana.cslab.ece.ntua.gr/tarbase/
RNAdb http://research.imb.uq.edu.au/rnadb/
PolymiRTS Database http://compbio.utmem.edu/miRSNP/
Noncoding RNA database http://biobases.ibch.poznan.pl/ncRNA/
RNALogo http://rnalogo.mbc.nctu.edu.tw/createlogo.html
DIANA - mirPath http://diana.cslab.ece.ntua.gr/pathways/index_multiple.php
miRDB http://mirdb.org/miRDB/
TransmiR http://202.38.126.151/hmdd/mirna/tf/
mirGen 2.0 http://diana.cslab.ece.ntua.gr/mirgen/
MAMI MetA Mir:target Inference http://mami.med.harvard.edu/