Sure thing.
And to answer your original question: there is a command-line tool in TPP
called batchcoverage (look in the bin/ directory) that calculates this
residue coverage -- and is the one used by ProteinProphet to populate that
attribute in protXML.
It needs an input file of the form:
Thanks Luis, that's helpful. For now I'll just use an older version of TPP
to get the coverage values.
Cheers,
Yasir
On Tuesday, March 28, 2023 at 6:46:58 PM UTC-4 Luis Mendoza wrote:
> Hello Yasir,
>
> We have recently identified a bug in ProteinProphet that mis-reports the
> coverage as
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
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
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
