Hello Yasir, We have recently identified a bug in ProteinProphet that mis-reports the coverage as zero for all proteins. This affects TPP versions 6.1.0 and 6.2.0. We will be releasing an update soon that corrects this and other bugs.
Even then, the value that is reported in protXML is the ratio of observed amino acids to total. There is no simple way to get the coverage based on the digestible portion of the protein, though we could think about adding that as a feature. Let me know if you would like to get a preview version of just ProteinProphet in advance of our release and I can post that separately, just specify if you use Linux or Windows. Alternatively, if you have a pre-6.1.0 version of TPP installed, you can run ProteinProphet and get the coverage values reported. Cheers, --Luis On Tue, Mar 28, 2023 at 2:50 PM Yasir Ahmed <[email protected]> wrote: > I guess I have another question about coverage: using ProtXMLViewer (which > is similar to the output from ProteinProphet), the coverage values are > almost always zero. For example, the example I show above has Obs/Dig of > 82%, but is showing percent coverage to be zero in the ProteinProphet > output. Any idea why? And can one get those Obs/Dig values? > > On Tuesday, March 28, 2023 at 5:23:06 PM UTC-4 Yasir Ahmed wrote: > >> Never mind, got it with ProtXMLViewer.pl (duh). >> >> On Tuesday, March 28, 2023 at 5:03:14 PM UTC-4 Yasir Ahmed wrote: >> >>> Greetings Friends, >>> >>> Is there a command line tool within the TPP that can output sequence >>> residue coverage percentages (Obs/Tot)? I can get those for individual >>> proteins using the ProtXMLViewer GUI (see attached image), but would like >>> to do this for every protein in my database. >>> >>> Cheers, >>> Yasir >>> >>> [image: Screen Shot 2023-03-28 at 4.29.18 PM.png] >>> >> -- > You received this message because you are subscribed to the Google Groups > "spctools-discuss" group. > To unsubscribe from this group and stop receiving emails from it, send an > email to [email protected]. > To view this discussion on the web visit > https://groups.google.com/d/msgid/spctools-discuss/bcc98ae1-0f89-4472-9a66-f0eeed496d5dn%40googlegroups.com > <https://groups.google.com/d/msgid/spctools-discuss/bcc98ae1-0f89-4472-9a66-f0eeed496d5dn%40googlegroups.com?utm_medium=email&utm_source=footer> > . > -- You received this message because you are subscribed to the Google Groups "spctools-discuss" group. To unsubscribe from this group and stop receiving emails from it, send an email to [email protected]. To view this discussion on the web visit https://groups.google.com/d/msgid/spctools-discuss/CACyS9brON3VABAs6GqpZXsQLkDszGufDLc2q%2BzsvMHSuBbfsVQ%40mail.gmail.com.
