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primer3-org / primer3

Primer3 is a command line tool to select primers for polymerase chain reaction (PCR).
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The oligotm tool has been outdated #23

Closed billzt closed 5 years ago

billzt commented 5 years ago

The oligotm tools still uses backward compatible calculation. Given this primer pair as an example:

Template: CCTGCATAATTCATGAAAAGAGCTTGCCATCCCTCCAGGTAGATATTAATTCTCGCAATCAGTGGTTGTAGTTCAGCAAAATTCAGTTTGGAGCTGGACAACGGAAGCCCGAGACTAGAGTACACCTGGGGGAAATTTTTCTACTTTGCAGTGGAGGATTGCTGCTACTGCTAGAGCTTGAGTTTCAGCACTATCTTGTGGAAGCCTGGAGTTCCTGCTGTAGCCTGTTAGCCATTGCTTTGGCTGTGATCTTGATGGAGCAAATCTGTAGCCGGAGGGACTAGCATAATATGATGAGGATC

Primer F:  AGACTAGAGTACACCTGGGG
Primer R: GCTCCATCAAGATCACAGCC

If you use oligotm, the Tm of primer F is 53.30 (still backward compatible calculation)

However, in the output of current version primer3 the Tm of primer F is 57.17

bioinfo-ut commented 5 years ago

Thanks.

We updated the default settings of oligotm. It now uses the same set of SantaLucia parameters as main primer3_core. This should fix the issue