pNovo Results Top 1

[lutfia95]

pNovo Results Top 1

[hbarsnes]

Hi Ahmad,

Due to licensing issues we stopped supporting pNovo in DeNovoGUI a while back. DeNovoGUI itself is also not really maintained anymore as both Novor and DirecTag can now instead be run via SearchGUI.

With regards to controlling the number of hits per spectrum, it seems like we never properly implemented this option in DeNovoGUI. However, DeNovoGUI is basically just a wrapper around the individual de novo algorithm command lines and you can therefore simply alter the pNovo parameter file and run the command line directly.

The pNovo command line looks something like this:

pNovo3.exe pnovo_params.txt ""

An example of a pNovo parameter file can be found in the DeNovoGUI-1.16.8\resources\pNovo\windows folder after you have run pNovo once via DeNovoGUI.

All you have to do is go down towards the end of the parameter file and change

#number of peptides reported
report_pep=10

into

#number of peptides reported
report_pep=1

and then rerun the pNovo command line.

Hopefully this should give you just one hit per spectrum in the output file.

Best regards,
Harald

[lutfia95]

Hey Harald,

thank you very much! yes I already did that, but the tool is not able to produce the aaScores for the different amino acids. No problem, thank you very much! From my side, we can close the issue.

Best,
Ahmad

[hbarsnes]

Hi Ahmad,

but the tool is not able to produce the aaScores for the different amino acids

Not sure which tool you are referring to here? Is this something that more recent versions of pNovo includes?

The only de novo algorithm that I know of that provides such scores is Novor.

Best regards,
Harald