BioSilicoList5
Diego Forero, MD, PhD
Personal Website
BioSilicoList
A comprehensive list of available in silico tools for genetics and genomics
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Resources for the analysis of genome-wide gene expression
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*Databases
NCBI GEO http://www.ncbi.nlm.nih.gov/sites/entrez?db=gds&cmd=search&term=
ArrayExpress http://www.ebi.ac.uk/microarray-as/ae/
BioGPS (Symatlas) http://biogps.gnf.org/?referer=symatlas#goto=welcome
Allen Brain Atlas http://brain-map.org/welcome.do;jsessionid=443E521520979E11B7191250398A64C3
Mouse Gene Prediction Database http://mgpd.med.utoronto.ca/
SMRI Online Genomics Database https://www.stanleygenomics.org/
NetAffx http://www.affymetrix.com/analysis/index.affx
Genevestigator https://www.genevestigator.ethz.ch/
GeneSapiens http://www.genesapiens.org/
Microarray Gene Expression Database Society http://www.mged.org
Affycomp II A Benchmark for Affymetrix GeneChip Expression Measures http://rafalab.biostat.jhsph.edu/AFFY2/TABLES.hgu/0.html
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*Servers/Programs
GEPAS http://gepas.bioinfo.cipf.es/
Babelomics http://babelomics.bioinfo.cipf.es/
DAVID http://david.abcc.ncifcrf.gov/summary.jsp
Expression Profiler http://www.ebi.ac.uk/expressionprofiler/
Brain Explorer http://mouse.brain-map.org/brainExplorer/index.html
Gene Set Enrichment Analysis (GSEA) http://www.broad.mit.edu/gsea/index.jsp
Clone/Gene ID Converter http://idconverter.bioinfo.cnio.es/
g:Profiler http://biit.cs.ut.ee/gprofiler/welcome.cgi
ID conversion tool http://david.abcc.ncifcrf.gov/conversion.jsp
Pathway-Express http://vortex.cs.wayne.edu/projects.htm
MTOM http://www.genetics.ucla.edu/labs/horvath/MTOM/
SiPaGene http://www.sipagene.de/sipagene/Find
WebGestalt http://bioinfo.vanderbilt.edu/webgestalt/
NIA Array Analysis http://lgsun.grc.nia.nih.gov/ANOVA/
WebArray http://www.webarraydb.org/webarray/index.html
CARMAweb https://carmaweb.genome.tugraz.at/carma/
oneChannelGUI http://www.bioconductor.org/packages/2.1/bioc/html/oneChannelGUI.html
GeneCruiser http://genecruiser.broad.mit.edu/genecruiser3/
GenePattern http://www.broad.mit.edu/cancer/software/genepattern/
PGE http://homes.esat.kuleuven.be/~bioiuser/pge/
Gene List Venn Diagram http://www.bioinformatics.org/gvenn/
List Sorter http://sites.google.com/site/dmbits/BITS-datamining/utilities/list-sorter
TableButler http://angiogenesis.dkfz.de/oncoexpress/software/tablebutler/
A-MADMAN http://compgen.bio.unipd.it/bioinfo/amadman/
MicroArray Retriever http://grenada.lumc.nl/HumaneGenetica/MaRe/
GeneSelector http://www.bioconductor.org/packages/bioc/vignettes/GeneSelector/inst/doc/GeneSelector.pdf
Available Computational Tools for Meta-analyses of Microarray Studies http://sites.google.com/site/compgensite/meta
Bioconductor Packages http://www.bioconductor.org/packages/release/Software.html (list in Google Docs)
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Sequence databases and analysis tools
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*Databases
UCSC Human http://genome.ucsc.edu/cgi-bin/hgGateway
Ensembl Human http://www.ensembl.org/Homo_sapiens/index.html
NCBI Human http://www.ncbi.nlm.nih.gov/projects/mapview/map_search.cgi?taxid=9606
Genecards http://genecards.org/
KEGG pathway http://www.genome.jp/kegg/pathway.html
Gene Ontology http://www.geneontology.org/
NCBI Homologene http://www.ncbi.nlm.nih.gov/sites/entrez?db=homologene
flybase http://flybase.bio.indiana.edu/
Homophila http://superfly.ucsd.edu/homophila/
flyatlas http://www.flyatlas.org/
Comparative Toxicogenomics Database http://ctd.mdibl.org/
Gene Aging Nexus http://gan.usc.edu/public/index.jsp
SynDB http://syndb.cbi.pku.edu.cn/sdb_index.php
WikiPathways http://www.wikipathways.org/index.php/WikiPathways
IntAct http://www.ebi.ac.uk/intact
NCBI BioSystems http://www.ncbi.nlm.nih.gov/biosystems
Pathway Interaction Database http://pid.nci.nih.gov/browse_pathways.shtml#NCI-Nature
REBASE http://rebase.neb.com/rebase/rebase.html
RTPrimerDB http://medgen.ugent.be/rtprimerdb/index.php
Quantitative PCR Primer Database (QPPD) http://web.ncifcrf.gov/rtp/gel/primerdb/
Primer Bank http://pga.mgh.harvard.edu/primerbank/
qPrimerDepot http://primerdepot.nci.nih.gov/
Satellog Database http://satellog.bcgsc.ca/
GeneCards Hot Genes http://www.genecards.org/hotCards.shtml
BioNumbers http://bionumbers.hms.harvard.edu/default.aspx
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*Servers/Programs
UCSC Blat http://genome.ucsc.edu/cgi-bin/hgBlat?command=start
NCBI Blast http://www.ncbi.nlm.nih.gov/genome/seq/BlastGen/BlastGen.cgi?taxid=9606
Primer3 http://frodo.wi.mit.edu/
Clustal W http://www.ebi.ac.uk/Tools/clustalw2/index.html
Reverse complement http://www.bioinformatics.org/sms/rev_comp.html
NEBcutter http://tools.neb.com/NEBcutter2/index.php
reverse complement http://arbl.cvmbs.colostate.edu/molkit/manip/
MFEprimer http://biocompute.bmi.ac.cn/MFEprimer/
PrimerStation http://ps.cb.k.u-tokyo.ac.jp/index.html
IDT OligoAnalyzer http://www.idtdna.com/analyzer/Applications/OligoAnalyzer/
BioEdit http://www.mbio.ncsu.edu/bioedit/bioedit.html
pDRAW32 http://www.acaclone.com/
Protein Movie Generator http://bioserv.rpbs.jussieu.fr/~autin/cgi-bin/PMG
geNorm http://medgen.ugent.be/~jvdesomp/genorm/
WebLogo http://weblogo.berkeley.edu/logo.cgi
Venny http://bioinfogp.cnb.csic.es/tools/venny/index.html
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*Data Mining in Genomics
Taverna http://taverna.sourceforge.net/
Galaxy http://g2.trac.bx.psu.edu/wiki
BioMart http://www.biomart.org/biomart/martview
myExperiment http://www.myexperiment.org/workflows
iTools http://cms.loni.ucla.edu/iTools/index.aspx
Orange http://www.ailab.si/orange/
Weka http://www.cs.waikato.ac.nz/~ml/weka/index.html
BioWeka http://bioweka.sourceforge.net/
BioMoby http://biomoby.open-bio.org/index.php/what-is-moby/publications
Remora http://lipm-bioinfo.toulouse.inra.fr/remora/cgi/remora.cgi
Seahawk http://biomoby.open-bio.org/CVS_CONTENT/moby-live/Java/docs/Seahawk.html
Sight http://www.bioinformatics.org/jSight/
Mobyle http://mobyle.pasteur.fr/cgi-bin/portal.py
ENDEAVOUR http://homes.esat.kuleuven.be/~bioiuser/endeavour/endeavour.php
ToppGene http://toppgene.cchmc.org/prioritization.jsp
Geneseeker http://www.cmbi.ru.nl/GeneSeeker/basic_form.html
G2D http://www.ogic.ca/projects/g2d_2/
Prospectr http://www.genetics.med.ed.ac.uk/prospectr/
SNOW http://snow.bioinfo.cipf.es/cgi-bin/snow.cgi
ToppNet http://toppgene.cchmc.org/network.jsp
GeneDistiller http://www.genedistiller.org/
Cipher http://bioinfo.au.tsinghua.edu.cn/cipher/cipher_search.php
GeneWanderer http://compbio.charite.de/genewanderer/GeneWanderer
TrAPSS2 http://putt.eng.uiowa.edu/trapss_research.html
DrugBank http://www.drugbank.ca/
Network Workbench http://nwb.slis.indiana.edu/index.html
iHOP http://www.ihop-net.org/UniPub/iHOP/
UniHI http://theoderich.fb3.mdc-berlin.de:8080/unihi/index
Chilibot http://www.chilibot.net/
SCAN http://scan.bsd.uchicago.edu/newinterface/about.html
HEFalMp http://sonorus.princeton.edu/hefalmp/
JSquid http://jsquid.sbc.su.se/
VECT http://www.complex.iastate.edu/download/Vect/index.html
KGG http://bioinfo.hku.hk:13080/kggweb/
GeneALaCart http://genecards.org/BatchQueries/index.php
EMMA http://www.emmanet.org/mutant_types.php
SNPExpress database http://people.genome.duke.edu/~dg48/SNPExpress/1_database.php
eQTL imputation http://www.sph.umich.edu/csg/liang/imputation/
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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
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/
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Tools for Literature Analysis
PubMed http://www.ncbi.nlm.nih.gov/pubmed/
PubMed Central http://www.pubmedcentral.nih.gov/
Google scholar http://scholar.google.be/schhp?hl=en&tab=ws
GoPubMed http://www.gopubmed.org/
PubCrawler http://pubcrawler.gen.tcd.ie/
citeulike http://www.citeulike.org/
mendeley http://www.mendeley.com/
Google patents http://www.google.com/patents
Scirus http://www.scirus.com/
FreePatentsOnline http://www.freepatentsonline.com/
BLAST in patents http://www.patentlens.net/sequence/blast/blast.html
espacenet http://ep.espacenet.com/advancedSearch?locale=en_EP
SCImago Journal & Country Rank http://www.scimagojr.com/
etBlast http://invention.swmed.edu/etblast/etblast.shtml
Deja vu http://spore.swmed.edu/dejavu/duplicate/
Nature Precedings http://precedings.nature.com/
PubGene http://www.pubgene.org/
HubMed http://www.hubmed.org/
PubMed Assistant http://metnet.vrac.iastate.edu/browser/
Journal Author Name Estimator http://biosemantics.org/jane/
BioText Search Engine http://biosearch.berkeley.edu/
H index calculator http://insitu.lri.fr/~roussel/projects/scholarindex/index.cgi
H index calculator http://quadsearch.csd.auth.gr/index.php?lan=1&s=2
PubMed-Citeulike script http://userscripts.org/scripts/show/2478
PublicationsList.org http://publicationslist.org/index.html
Journals in Bioinformatics http://www.bioinformatics.org/wiki/Journals
Protocol Online http://www.protocol-online.org/
Nature Protocols http://www.nature.com/nprot/index.html
WolframAlpha http://www65.wolframalpha.com/
Google Squared http://www.google.com/squared/
eigenfactor.org http://www.eigenfactor.org/
PubNet http://pubnet.gersteinlab.org/
TagCrowd http://www.tagcrowd.com/
Tag Cloud Generator http://www.tagcloud-generator.com/generator.php#anker
is.gd URL shortener http://is.gd/
Distribution of Impact Factors in pdf
Comparison of journals http://sites.google.com/site/neurocienciaspanam/journals-1
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Extended lists of servers/programs
Bioinformatics Links Directory http://bioinformatics.ca/links_directory
Genetic analysis programs http://linkage.rockefeller.edu/soft/
hum-molgen.org: bioinformatic tools http://hum-molgen.org/bioinformatics/
BioCatalogue http://www.biocatalogue.org/
BioInformatics Resource Inventory (B.I.R.I.) http://edelman.dia.fi.upm.es/biri/
BMC Databases -Genetics http://databases.biomedcentral.com/browsesubject/?sub_id=1007
tools at bioinformatics.org http://www.bioinformatics.org/softwaremap/?form_cat=2
NAR web server 2009 http://nar.oxfordjournals.org/content/vol37/suppl_2/index.dtl
NAR database 2009 http://nar.oxfordjournals.org/content/vol37/suppl_1/index.dtl
NAR web server 2008 http://nar.oxfordjournals.org/content/vol36/suppl_2/index.dtl
NAR database 2008 http://nar.oxfordjournals.org/content/vol36/suppl_1/index.dtl
NAR web server 2007 http://nar.oxfordjournals.org/content/vol35/suppl_2/index.dtl
NAR database 2007 http://nar.oxfordjournals.org/content/vol35/suppl_1/index.dtl
OpenHelix Search http://openhelix.eu/index.shtml
Gene Quantification http://www.gene-quantification.info/
Primer design http://www.humgen.nl/primer_design.html
Microarray programs http://engr.smu.edu/~mfonten/research/MAsoftware.html
Genetic variation databases http://www.humgen.nl/SNP_databases.html
Mutalyzer-Sequence variant nomenclature check http://www.lovd.nl/mutalyzer/1.0.1/
List of Biomedical Text Mining Tools http://arrowsmith.psych.uic.edu/arrowsmith_uic/tools.html
SNPAcquisition http://variome.kobic.re.kr/SNPatWEB/Wiki.jsp?page=SNPAcquisition
Tools for Next Generation Sequencing http://www.oxfordjournals.org/our_journals/bioinformatics/nextgenerationsequencing.html
Open Bioinformatics Foundation http://www.open-bio.org/wiki/Main_Page
Sequence Manipulation Suite http://www.bioinformatics.org/sms2/
Blogs-Bioinformatics http://blogs.scientifik.info/bioinformatics/?p=66
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Bio-Programming
bioJava http://biojava.org/
bioPerl http://www.bioperl.org/
bioPython http://biopython.org/
BioPHP http://www.biophp.org/
BioC++ http://biocpp.sourceforge.net/
Bio++ http://162.38.181.25/BioPP/
BioSQL http://biosql.org/wiki/Main_Page
R environment www.r-project.org
Rpad http://www.rpad.org/Rpad/
R Commander http://socserv.mcmaster.ca/jfox/Misc/Rcmdr
R Reference Card http://cran.r-project.org/doc/contrib/Short-refcard.pdf
Biotool2Web http://www.imib.med.uni-rostock.de/biotoolwww/biotool2web/index.html
Programming Languages Comparison http://www.ohloh.net/languages/compare
hhttp://atgu.mgh.harvard.edu/plinkseq/index.shtml
http://bioinf.uta.fi/PON-P/index.shtml
http://bioinfo.mc.vanderbilt.edu/NGS/index.html
http://biq-analyzer-ht.bioinf.mpi-inf.mpg.de/
http://braun.tx0.org/PoDA/
http://cbc.case.edu/dir/
http://cbrc.kaust.edu.sa/dpore
http://code.google.com/p/fstsnp-hapmap3/
http://dna.leeds.ac.uk/cpgviewer/
http://elephant.embl.de/enrichnet/index.php
http://evs.gs.washington.edu/EVS/
http://fastsnp.ibms.sinica.edu.tw/pages/input_novel.jsp
http://genetics.bwh.harvard.edu/pph2/
http://genome.igib.res.in/mirlovd
http://gvs.gs.washington.edu/SeattleSeqAnnotation/
http://homes.esat.kuleuven.be/~bioiuser/gpp/index.php
http://klab.smpp.northwestern.edu/h-index.html
http://kobas.cbi.pku.edu.cn/home.do
http://metamoodics.igm.jhmi.edu/
http://mutpred.mutdb.org/
http://nar.oxfordjournals.org/cgi/content/abstract/35/18/6227
http://onlinelibrary.wiley.com/doi/10.1002/0471142905.hg0920s60/full
http://pfs.nus.edu.sg
http://quma.cdb.riken.jp/
http://research.nhgri.nih.gov/software/VarSifter/
http://rostlab.org/services/snap/submit
http://snps-and-go.biocomp.unibo.it/snps-and-go/
http://snpsyn.biolab.si/examples.html
http://sourceforge.net/projects/atlas2/
http://sourceforge.net/projects/snpman/files/
http://statgenpro.psychiatry.hku.hk/limx/kggseq/
http://wannovar.usc.edu/
http://wiki.chasmsoftware.org/index.php/Main_Page
http://www.bioextract.org
http://www.chibi.ubc.ca/Gemma/home.html
http://www.cymate.org/
http://www.ebiomed.org/ncFANs/
http://www.esat.kuleuven.be/pinta/
http://www.gene-quantification.info/
http://www.genomespace.org/
http://www.gwaspi.org/
http://www.mh-hannover.de/929.html
http://www.microrna.gr/microT-v4
http://www.molgen.mpg.de/~bertram/welcome.html
http://www.mutadatabase.org/
http://www.mutationtaster.org/
http://www.ncbi.nlm.nih.gov/sites/GeneTests/
http://www.ncbi.nlm.nih.gov/tools/primer-blast/
http://www.ogic.ca/projects/peer2ref/
http://www.paris-neuroscience.fr/index-uk.php
http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1001130 GWAS AD
http://www.rostlab.org/services/snpdbe/
http://www.tavaxy.org
http://www.udifmv.ulg.ac.be/genmol/Department/Useful_links/nrg1803.pdf
http://www2.cancer.ucl.ac.uk/Parkinson_Db2/index.php
http://www-stat.stanford.edu/~tibs/ElemStatLearn/
https://bitbucket.org/fubar/galaxytoolfactory
https://insilicodb.org/