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The Protein Coverage Summarizer can be used to determine the percent of the residues in each protein sequence that have been identified, based on a list of identified peptides. A graphical user interface (GUI) is provided to allow the user to select the input files, set the options, and browse the coverage results.
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PeptideToProteinMapper
ProteinCoverageSummarizer
ProteinCoverageSummarizer_Installer
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ProteinCoverageSummarizerGUI.sln
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ProteinCoverageSummarizerGUI_x64.sln
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ProteinCoverageSummarizerGUI_x64.vbproj
README.md
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app.config
clsProteinCoverageSummarizerRunner.vb
modMain.vb

README.md

Protein Coverage Summarizer

The Protein Coverage Summarizer can be used to determine the percent of the residues in each protein sequence that have been identified.

The program requires two input files:

  • a file with protein names and protein sequences (optionally with protein description). This can be a tab-delimited text file or a FASTA file
  • a file with peptide sequences and optionally also protein names for each peptide

A graphical user interface (GUI) is provided to allow the user to select the input files, set the options, and browse the coverage results. The results browser displays the protein sequences, highlighting the residues that were present in the peptide input file, and providing sequence coverage stats for each protein.

Console Version Syntax

ProteinCoverageSummarizerGUI.exe
  /I:PeptideInputFilePath /R:ProteinInputFilePath [/O:OutputDirectoryName]
  [/P:ParameterFilePath] [/G] [/H] [/M] [/K] [/Debug] [/KeepDB]

The input file path can contain the wildcard character *. If a wildcard is present, the same protein input file path will be used for each of the peptide input files matched.

The output directory name is optional. If omitted, the output files will be created in the same directory as the input file. If included, a subdirectory is created with the name OutputDirectoryName.

The parameter file path is optional. If included, it should point to a valid XML parameter file.

Use /G to ignore I/L differences when finding peptides in proteins or computing coverage.

Use /H to suppress (hide) the protein sequence in the _coverage.txt file.

Use /M to enable the creation of a protein to peptide mapping file.

Use /K to skip protein coverage computation steps

Use /Debug to keep the console open to see additional debug messages

Use /KeepDB to keep the SQLite database after processing (by default it is deleted)

Contacts

Written by Matthew Monroe and Nikša Blonder for the Department of Energy (PNNL, Richland, WA) in 2005
E-mail: matthew.monroe@pnnl.gov or proteomics@pnnl.gov
Website: https://omics.pnl.gov or https://panomics.pnl.gov/

License

The Protein Coverage Summarizer is licensed under the 2-Clause BSD License; you may not use this file except in compliance with the License. You may obtain a copy of the License at https://opensource.org/licenses/BSD-2-Clause

Copyright 2018 Battelle Memorial Institute

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