PCR primer database
- GETPrime 2.0 (http://bbcftools.epfl.ch/getprime)
- RTPrimerDB (http://www.rtprimerdb.org)
- PrimerBank (https://pga.mgh.harvard.edu/primerbank)
- qPrimerDepot (https://primerdepot.nci.nih.gov)
- DATFAP (http://cgi-www.daimi.au.dk/cgi-chili/datfap/frontdoor.py)
- MRPrimerV (http://mrprimerv.com)
- MRPrimerW (http://mrprimerw.com)
- methPrimerDB (https://methprimerdb.cmgg.be)
- FlyPrimerBank (http://www.flyrnai.org/flyprimerbank)
- AtRTPrimer (http://atrtprimer.kaist.ac.kr)
Genome sequence database
- Ensembl (http://www.ensembl.org/index.html)
- Phytozome (https://phytozome.jgi.doe.gov/pz/portal.html)
- UCSC (https://genome.ucsc.edu)
- PLAZA (http://bioinformatics.psb.ugent.be/plaza)
- PGDD (http://chibba.agtec.uga.edu/duplication)
- Gramene (http://www.gramene.org)
- Sol Genomics Network (https://www.sgn.cornell.edu)
- Pepper Genome Platform (http://peppergenome.snu.ac.kr)
- Legume Information System (https://legumeinfo.org)
- Cucurbit Genomics Database (http://www.icugi.org)
- Genome Database for Rosaceae (https://www.rosaceae.org)
- InsectBase (http://www.insect-genome.com)
- SilkPathDB (http://silkpathdb.swu.edu.cn)
- VectorBase (https://www.vectorbase.org)
PCR primer design program
- Primer3 (http://primer3.sourceforge.net)
- Primer3Plus (http://www.bioinformatics.nl/cgi-bin/primer3plus/primer3plus.cgi)
- MFEprimer 2.0 (http://biocompute.bmi.ac.cn/CZlab/MFEprimer-2.0)
- MRPrimer (http://mrprimer.com)
- Primer-BLAST (https://www.ncbi.nlm.nih.gov/tools/primer-blast)
- BatchPrimer3 v1.0 (http://probes.pw.usda.gov/batchprimer3)
- MPprimer (http://biocompute.bmi.ac.cn/MPprimer)
- VizPrimer (http://biocompute.bmi.ac.cn/CZlab/VizPrimer)
- ePCR (https://www.ncbi.nlm.nih.gov/tools/epcr)
- BBTools (http://jgi.doe.gov/data-and-tools/bbtools)
- PerlPrimer (http://perlprimer.sourceforge.net/index.html)
- PCRTiler (http://pcrtiler.genap.ca/PCRTiler)
- PRIMEGENS (http://primegens.org)
- ConservedPrimers 2.0 (http://probes.pw.usda.gov/ConservedPrimers)
- Oligo 7 (http://www.oligo.net/index.html)
- QuantPrime (http://quantprime.mpimp-golm.mpg.de)
- The PCR Suite (http://pcrsuite.cse.ucsc.edu)
- PrimerStation (http://ps.cb.k.u-tokyo.ac.jp/index.html)
- primers4clades (http://floresta.eead.csic.es/primers4clades)
- In-Silico PCR (http://genome.ucsc.edu/cgi-bin/hgPcr?db=hg18)
- CODEHOP (http://blocks.fhcrc.org/codehop.html)
- TestPrime 1.0 (https://www.arb-silva.de/search/testprime)