PCR primer database

1. GETPrime 2.0 (http://bbcftools.epfl.ch/getprime)
2. RTPrimerDB (http://www.rtprimerdb.org)
3. PrimerBank (https://pga.mgh.harvard.edu/primerbank)
4. qPrimerDepot (https://primerdepot.nci.nih.gov)
5. DATFAP (http://cgi-www.daimi.au.dk/cgi-chili/datfap/frontdoor.py)
6. MRPrimerV (http://mrprimerv.com)
7. MRPrimerW (http://mrprimerw.com)
8. methPrimerDB (https://methprimerdb.cmgg.be)
9. FlyPrimerBank (http://www.flyrnai.org/flyprimerbank)
10. AtRTPrimer (http://atrtprimer.kaist.ac.kr)

 

Genome sequence database

1.  Ensembl (http://www.ensembl.org/index.html)
2. Phytozome (https://phytozome.jgi.doe.gov/pz/portal.html)
3. UCSC (https://genome.ucsc.edu)
4. PLAZA (http://bioinformatics.psb.ugent.be/plaza)
5. PGDD (http://chibba.agtec.uga.edu/duplication)
6. Gramene (http://www.gramene.org)
7. Sol Genomics Network (https://www.sgn.cornell.edu)
8. Pepper Genome Platform (http://peppergenome.snu.ac.kr)
9. Legume Information System (https://legumeinfo.org)
10. Cucurbit Genomics Database (http://www.icugi.org)
11. Genome Database for Rosaceae (https://www.rosaceae.org)
12. InsectBase (http://www.insect-genome.com)
13. SilkPathDB (http://silkpathdb.swu.edu.cn)
14. VectorBase (https://www.vectorbase.org)

 

PCR primer design program

1. Primer3 (http://primer3.sourceforge.net)
2. Primer3Plus (http://www.bioinformatics.nl/cgi-bin/primer3plus/primer3plus.cgi)
3. MFEprimer 2.0 (http://biocompute.bmi.ac.cn/CZlab/MFEprimer-2.0)
4. MRPrimer (http://mrprimer.com)
5. Primer-BLAST (https://www.ncbi.nlm.nih.gov/tools/primer-blast)
6. BatchPrimer3 v1.0 (http://probes.pw.usda.gov/batchprimer3)
7. MPprimer (http://biocompute.bmi.ac.cn/MPprimer)
8. VizPrimer (http://biocompute.bmi.ac.cn/CZlab/VizPrimer)
9. ePCR (https://www.ncbi.nlm.nih.gov/tools/epcr)
10. BBTools (http://jgi.doe.gov/data-and-tools/bbtools)
11. PerlPrimer (http://perlprimer.sourceforge.net/index.html)
12. PCRTiler (http://pcrtiler.genap.ca/PCRTiler)
13. PRIMEGENS (http://primegens.org)
14. ConservedPrimers 2.0 (http://probes.pw.usda.gov/ConservedPrimers)
15. Oligo 7 (http://www.oligo.net/index.html)
16. QuantPrime (http://quantprime.mpimp-golm.mpg.de)
17. The PCR Suite (http://pcrsuite.cse.ucsc.edu)
18. PrimerStation (http://ps.cb.k.u-tokyo.ac.jp/index.html)
19. primers4clades (http://floresta.eead.csic.es/primers4clades)
20. In-Silico PCR (http://genome.ucsc.edu/cgi-bin/hgPcr?db=hg18)
21. CODEHOP (http://blocks.fhcrc.org/codehop.html)
22. TestPrime 1.0 (https://www.arb-silva.de/search/testprime)