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dr-joe-wirth / primerForge

software to identify primers that can distinguish genomes
Apache License 2.0
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the result of primerForge #15

Closed aiqubo closed 2 months ago

aiqubo commented 3 months ago

Hi joe,

Thank you for your primerForge, I have some confusion for the result of primerForge,

Can this software input the following sequence as a ingroup file, and output some primers that can cover the following genomes? It seem that the result file contain a large number of primers, but none of them can cover the entire genome.

'''

CP012805.1 Streptococcus anginosus strain J4211, complete genome CP044219.1 Streptococcus mutans strain NCH105 plasmid pMut1, complete sequence CP044220.1 Streptococcus mutans strain NCH105 plasmid pMut2, complete sequence CP044221.1 Streptococcus mutans strain NCH105 chromosome, complete genome CP066055.1 Streptococcus constellatus strain FDAARGOS_1015 chromosome, complete genome CP067992.1 Streptococcus mitis strain S022-V7-A3 chromosome, complete genome FR873482.1 Streptococcus salivarius JIM8777 complete genome LS483436.1 Streptococcus intermedius strain NCTC11324 genome assembly, chromosome: 1 NZ_LS483346.1 Streptococcus sanguinis strain NCTC11085 chromosome 1, complete sequence

'''

Qubo

result.xlsx

dr-joe-wirth commented 3 months ago

@aiqubo I'm not sure I understand your question. Looking at your results, it appears you ran primerForge on a single genome. It is designed to take multiple genomes at once and find shared primer pairs that can be used in all the input genomes.

It seems the result file contain a large number of primers, but none of them can cover the entire genome.

I'm not sure what you're asking. Primers are used in PCR and are not intended to cover the entire genome. They should amplify specific regions of the genome. It is not possible to design a pair of primers that "can cover the entire genome."

If you need more assistance, please include the log file.

aiqubo commented 2 months ago

Thank you for your quick response to my question, I want to design a pair of primers that can amplify the following 7 sequences of Streptococcus species

''' CP012805.1 Streptococcus anginosus strain J4211, complete genome CP044221.1 Streptococcus mutans strain NCH105 chromosome, complete genome CP066055.1 Streptococcus constellatus strain FDAARGOS_1015 chromosome, complete genome CP067992.1 Streptococcus mitis strain S022-V7-A3 chromosome, complete genome FR873482.1 Streptococcus salivarius JIM8777 complete genome LS483436.1 Streptococcus intermedius strain NCTC11324 genome assembly, chromosome: 1 NZ_LS483346.1 Streptococcus sanguinis strain NCTC11085 chromosome 1, complete sequence '''

If they don’t find a common primer probe, will they automatically find a part of them?

dr-joe-wirth commented 2 months ago

Sure that seems like it would work.