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Pipasic specifications

Information


Unique identifier OMICS_07732
Name Pipasic
Alternative name Peptide intensity-weighted proteome abundance similarity correction
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
License BSD 2-clause “Simplified” License
Computer skills Advanced
Stability Stable
Maintained Yes

Versioning


No version available

Maintainer


  • person_outline Bernhard Renard

Publication for Peptide intensity-weighted proteome abundance similarity correction

Pipasic citations

 (3)
call_split

Metaproteomic analysis of human gut microbiota: where are we heading?

2017
J Biomed Sci
PMCID: 5469034
PMID: 28606141
DOI: 10.1186/s12929-017-0342-z
call_split See protocol

[…] -MS/MS) is particularly useful to reduce sample complexity and improve protein identification. The final and fairly demanding stage for metaproteomics is data analysis. Several software tools such as Pipasic [], MetaProteomeAnalyzer [] and Unipept [] have been developed to facilitate metaproteomic data analysis. One of the key elements for a successful metaproteomic study is the availability of a […]

library_books

Soil and leaf litter metaproteomics—a brief guideline from sampling to understanding

2016
PMCID: 5026301
PMID: 27549116
DOI: 10.1093/femsec/fiw180

[…] e reduced to the lowest common anchor (LCA) (Fig. ). The Unipept web application provides a robust LCA approach considering all occurrences of identified tryptic peptides in UniprotKB. Alternatively, Pipasic estimates the peptide level similarity between reference proteomes allowing differentiation on strain level. The PROPHANE web service provides a combined fully automated workflow for both (i) […]

library_books

Accelerating precision biology and medicine with computational biology and bioinformatics

2014
Genome Biol
PMCID: 4709972
PMID: 25316263
DOI: 10.1186/s13059-014-0450-y

[…] s a role in disease diagnoses but is limited by the presence of highly similar protein sequences among related organisms. Bernhard Renard (Robert Koch Institute, Germany) presented an algorithm named Pipasic that corrects peptide proteome abundance after modeling the aggregated abundance by similar protein sequences. He demonstrated more-accurate quantification of peptides for mixed species in com […]

Citations

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Pipasic institution(s)
Research Group Bioinformatics (NG4), Robert Koch Institute, Berlin, Germany

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