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biologger / speciesprimer

The SpeciesPrimer pipeline is intended to help researchers finding specific primer pairs for the detection and quantification of bacterial species in complex ecosystems.
GNU General Public License v3.0
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Decode the gene name from the results table #7

Closed Lorenzomicro closed 3 years ago

Lorenzomicro commented 3 years ago

Good morning, I finally got a 19 pair of primers for my Enterobacter kobei and I am very happy about it. But I have another question now ;) In the _primer file, for every set of primer, a gene name is associated with them. In some case it correspond to a protein (wecD) and is possible to track it down and maybe use that as a criteria to reduce the number of primer to test. In other case is just a default name like g2895_1, g20472_3, g20472_3, g20556_2, g1516_4, g20637_2. Are this number something like hypothetical protein, so I can't associate them with any protein ?

Cheers Lorenzo

biologger commented 3 years ago

Hi Lorenzo,

Yes, the primer names contain the name of the gene, in the case of g.... these are hypothetical proteins named "group_{number}" by Prokka.

Cheers, Matt

Lorenzomicro commented 3 years ago

Great! Thanks Matt

Cheers Lorenzo