I.1. HSPH Department of Biostatistics

http://www.hsph.harvard.edu/Academics/bio/

I.2. HSPH Department of Epidemiology

http://www.hsph.harvard.edu/epidemiology/

I.3. Dana-Farber/Harvard Cancer Center

http://www.dfhcc.harvard.edu/

I.4. Breast and Prostate Cancer Cohort Consortium

http://epi.grants.cancer.gov/BPC3/

 I.5. National Cancer Institute Cancer Genetic Markers of Susceptibility (NCI CGEMS)

http://cgems.cancer.gov/

II.1. NCBI Tools

http://www.ncbi.nlm.nih.gov/Tools/

II.2. EBI Tools

http://www.ebi.ac.uk/Tools/

II.3. SNP Tools

• SNPbox

  http://www.snpbox.org/

   

• SNPper

  http://snpper.chip.org/

   

• SNPHunter

  http://www.hsph.harvard.edu/ppg/software.htm

   

• SNPServer

  http://hornbill.cspp.latrobe.edu.au/cgi
  binpub/autosnip/index_autosnip.pl

   

• SNP Cutter

  http://bioinfo.bsd.uchicago.edu/SNP_cutter.htm

   

• SNPAnalyzer

  http://www.istech.info/istech/board/login_form.jsp

   

• nsSNPAnalyzer

  http://snpanalyzer.utmem.edu/

   

• rSNP Tools

  http://wwwmgs.bionet.nsc.ru/mgs/systems/rsnp/

   

• Structure

  http://pritch.bsd.uchicago.edu/structure.html

   

• GOLD

  http://www.sph.umich.edu/csg/abecasis/GOLD/

   

• BLAST2

  http://lpgws.nci.nih.gov/perl/blast2

   

• novoSNP

  http://www.molgen.ua.ac.be/bioinfo/novosnp/

   

• PolyBayes

  http://genomeold.wustl.edu/groups/informatics/
  software/polybayes/

   

• PolyPhred

  http://droog.mbt.washington.edu/PolyPhred.html

   

• PupaSNP Finder

  http://www.pupasnp.org/

   

II.4. DNA Sequence Analysis Tools

• Restriction Mapper

  http://www.restrictionmapper.org/

   

• Web Cutter

  http://www.ccsi.com/firstmarket/firstmarket/
  cutter/cut2.html

   

• RepeatMasker

  http://www.repeatmasker.org/

   

• Graphical Codon Usage Analyzer

  http://gcua.schoedl.de/

   

• VISTA

  http://genome.lbl.gov/vista/index.shtml

   

• SeqVISTA

  http://zlab.bu.edu/SeqVISTA/

   

• Phylogenetic Programs

  http://evolution.genetics.washington.edu/
  phylip/software.html

   

II.5. Finding Transcriptional Elements

• Promoter Identification

  http://www.fruitfly.org/seq_tools/promoter.html

   

• WWW Signal Scan

  http://bimas.dcrt.nih.gov/molbio/signal/

   

• RepeatMasker

  http://www.repeatmasker.org/

   

• Human Core Promoter Finder

  http://rulai.cshl.org/tools/genefinder/
  CPROMOTER/human.htm

   

• Human Poly(A) Site Prediction

  http://rulai.cshl.org/tools/polyadq/
  polyadq_form.html

   

• Human Promoter Mapping Using CpG Islands

  http://rulai.cshl.org/tools/CpG_promoter/

   

• Human first-exon and promoter prediction program

  http://rulai.cshl.org/tools/FirstEF/

   

• Exon Splicing Enhancer Finder

  http://rulai.cshl.edu/tools/ESE/

   

II.6. Finding tRNA

• Exon Splicing Enhancer Finder

  http://www.genetics.wustl.edu/eddy/tRNAscan-SE/

   

• FAStRNA

  http://bioweb.pasteur.fr/seqanal/interfaces/
  fastrna.html

II.7. Primer Design

• Primer3

  http://frodo.wi.mit.edu/cgi-bin/primer3/
  primer3_www.cgi

   

• SNP Primers

  http://www2.eur.nl/fgg/kgen/primer/
  SNP_Primers.html

   

• Genomic DNA Primers

  http://www2.eur.nl/fgg/kgen/primer/
  Genomic_Primers.html

   

• cDNA Primers

  http://www2.eur.nl/fgg/kgen/primer/
  cDNA_Primers.html

   

• Overlapping Primers

  http://www2.eur.nl/fgg/kgen/primer/
  Overlapping_Primers.html

   

II.8. Multiple Sequence Alignment Tools

•  ClustalW

  http://searchlauncher.bcm.tmc.edu/multi-align/
  Options/clustalw.html

• MAP

  http://searchlauncher.bcm.tmc.edu/multi-align/
  Options/map.html

   

• PIMA

  http://searchlauncher.bcm.tmc.edu/multi-align/
  Options/pima.html

   

• MultAlin

  http://prodes.toulouse.inra.fr/multalin/
  multalin.html
  
  

III.1. Primary Sequence Databases

• EMBL

  http://www.ebi.ac.uk/embl/

   

• GenBank

  http://www.ncbi.nlm.nih.gov/Genbank/index.html

   

• DDBJ

  http://www.ddbj.nig.ac.jp/

   

III.2. SNP Databases

• NCBI dbSNP

  http://www.ncbi.nlm.nih.gov/SNP/

   

• SNP500Cancer (CGAP)

  http://snp500cancer.nci.nih.gov

   

• HGVbase

  http://hgvbase.cgb.ki.se/

• SNP500Cancer (CGAP)

  http://snp500cancer.nci.nih.gov

   

• IIPGA

  http://innateimmunity.net/

 

• SeattleSNPs

  http://pga.mbt.washington.edu/

 

• GeneSNPs

  http://www.genome.utah.edu/genesnps/

 

• NIEHS SNPs

  http://egp.gs.washington.edu/

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