Protein Coverage Summarizer specifications

Information


Unique identifier OMICS_14941
Name Protein Coverage Summarizer
Software type Package/Module
Interface Command line interface, Graphical user interface
Restrictions to use None
Input data The protein names and protein sequences, the peptide sequences and optionally the protein name associated with each peptide sequence.
Operating system Windows
License Apache License version 2.0
Computer skills Advanced
Stability Stable
Maintained Yes

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Maintainer


  • person_outline Matthew Monroe <>

Protein Coverage Summarizer in publications

 (4)
PMCID: 4712314
PMID: 26870752
DOI: 10.1016/j.dib.2015.11.055

[…] the id mapping functionality of the uniprot website (http://www.uniprot.org/uploadlists/). percentage sequence coverage, and numbers of non-distinct and distinct peptides were calculated using the protein coverage summarizer program from the pan-omics research division of the pacific northwest national laboratory (http://omics.pnl.gov/software/protein-coverage-summarizer). uniprot ids […]

PMCID: 3189872
PMID: 21929753
DOI: 10.1186/1477-5956-9-56

[…] oxidation of methionine modifications. only identities from mascot with three or more peptides were considered., as several peptides from a protein were identified from different q-tof analyses, protein coverage summarizer software [] was used to determine the percentage of the residues in each protein sequence that was identified (coverage column in table )., plasma samples were diluted […]

PMCID: 2816023
PMID: 19755719
DOI: 10.1074/mcp.M900008-MCP200

[…] was generated (see supplemental tables 4 and 5) along with a fasta file containing the relevant protein sequences. the percent coverage was then calculated for each protein using the application “protein coverage summarizer,” which was obtained from the pacific northwest national laboratory., to assign a statistical probability that each bait-prey interaction was specific, an application […]

PMCID: 2570797
PMID: 18974882
DOI: 10.1371/journal.ppat.1000195

[…] of p. falciparum peptides. to remove redundancy on the protein level and to uniquely assign peptides to one protein, the peptides were remapped to plasmodb 5.3 annotated genome using the program protein coverage summarizer (http://ncrr.pnl.gov/software/). the collected peptide list of this study (malaria peptides identified in the mosquito stages) is available in ., to determine the protein […]


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Protein Coverage Summarizer funding source(s)
This work was supported by the NIH National Center for Research Resources (Grant RR018522), the W.R. Wiley Environmental Molecular Science Laboratory (a national scientific user facility sponsored by the U.S. Department of Energy's Office of Biological and Environmental Research and located at PNNL), and the National Institute of Allergy and Infectious Diseases (NIH/DHHS through interagency agreement Y1-AI-4894-01).

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