EPRIMER3
EPRIMER3: Is the EMBOSS version of PRIMER3. It lacks the beautiful interface of PRIMER3, but can be used to pick PCR primers and hybridization oligos. Primer3 picks primers for PCR reactions, considering as criteria: - oligonucleotide melting temperature, size, GC content, and primer-dimer possibilities - PCR product size - positional constraints within the source sequence - miscellaneous other constraints All of these criteria are user-specifiable as constraints, and some are specifiable as terms in an objective function that characterizes an optimal primer pair. Part of Emboss.
ADVICE FOR PICKING PRIMERS: The Emboss team suggests referring to: Wojciech Rychlik (1993) "Selection of Primers for Polymerase Chain Reaction" in BA White, Ed., "Methods in Molecular Biology, Vol. 15: PCR Protocols: Current Methods and Applications", pp 31-40, Humana Press, Totowa NJ.
If you use this tool, please cite: Rozen S., and Skaletsky, H. J. (2000) "Primer3 on the WWW for general users and for biologist programmers." In: Krawetz S, Misener S (eds) Bioinformatics Methods and Protocols: Methods in Molecular Biology. Humana Press, Totowa, NJ, pp 365-386
If you use EMBOSS, please cite: Rice, P, Longden, I, and Bleasby, A (2000) " EMBOSS: The European Molecular Biology Open Software Suite" Trends in Genetics 16, (6) 276--277.
Manual: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/eprimer3.html
INPUT = DNA Sequences.