BioSilicoList5

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/

SIFT http://sift.jcvi.org/

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

Rfam http://rfam.sanger.ac.uk

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/