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Peppy specifications

Information


Unique identifier OMICS_06910
Name Peppy
Software type Pipeline/Workflow
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Computer skills Advanced
Stability Stable
Maintained Yes

Versioning


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Publication for Peppy

Peppy citations

 (4)
library_books

Comparative genomics of the wheat fungal pathogen Pyrenophora tritici repentis reveals chromosomal variations and genome plasticity

2018
BMC Genomics
PMCID: 5913888
PMID: 29685100
DOI: 10.1186/s12864-018-4680-3

[…] spectrometry (LTQ Orbitrap Velos or XL).Spectra were searched against database of six-frame translated genome, a reverse decoy peptide database and contaminant sequences of keratin and trypsin using Peppy™ (2015) []: maximumFDR 0.01; precursorTolerance 2000; fragmentTolerance 300; Digestion rules - cleavageAcid R, cleavageAcid K, numberOfMissedCleavages 1; static mods -modC 57.021464, variable mo […]

library_books

FSPP: A Tool for Genome Wide Prediction of smORF Encoded Peptides and Their Functions

2018
Front Genet
PMCID: 5896265
PMID: 29675032
DOI: 10.3389/fgene.2018.00096

[…] ify the proper expressed SEPs. FSPP has integrated RiboTaper () to process Ribo-seq and resulted in the translation production sets including SEPs and other proteins longer than 100. On another hand, Peppy () was used to match the MS spectra to the reference genome and obtained the best genomic location for each spectrum. At last, FSPP intersected the two results from Ribo-seq and mass spectrometr […]

library_books

Metaproteomics of complex microbial communities in biogas plants

2015
PMCID: 4554464
PMID: 25874383
DOI: 10.1111/1751-7915.12276

[…] interaction might not be an ‘one way road’. In particular, ‘proteogenomics’ approaches might be applied to assist the annotation of metagenome data using the recently published proteogenomic software Peppy (Risk et al., ). Another option might be the combination of flow cytometry and metaproteomics (Jehmlich et al., ) as cell sorting enriches microbial subpopulations and therefore reduces complexi […]

library_books

Flexible and Accessible Workflows for Improved Proteogenomic Analysis Using the Galaxy Framework

2014
J Proteome Res
PMCID: 4261978
PMID: 25301683
DOI: 10.1021/pr500812t

[…] ,,− have emerged recently to support such analyses, offering tools for steps within one or more of the modules defined in Figure . Platforms expressly designed for proteogenomic analysis, such as the Peppy software, are also emerging. Although none of these software tools offer the combined flexibility, accessibility, and completeness of our Galaxy-based workflow, many of these programs are well-d […]

Citations

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Peppy institution(s)
Department of Biochemistry and Biophysics, UNC School of Medicine, Chapel Hill, NC, USA

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