Metaproteomic analysis allows studying the interplay of organisms or functional groups and has become increasingly popular also for diagnostic purposes. However, difficulties arise due to the high sequence similarity between related organisms. Further, the state of conservation of proteins between species can be correlated with their expression level which can lead to significant bias in results and interpretation. These challenges are similar but not identical to the challenges arising in the analysis of metagenomic samples and require specific solutions.

pipasic (peptide intensity-weighted proteome abundance similarity correction) is a tool which corrects identification and spectral counting based quantification results using peptide similarity estimation and expression level weighting within a non-negative lasso framework. pipasic has distinct advantages over approaches only regarding unique peptides or aggregating results to the lowest common ancestor.

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Categories

Bio-Informatics

License

BSD License

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pipasic Web Site

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Additional Project Details

Operating Systems

Linux, BSD

Intended Audience

Science/Research

User Interface

Command-line

Programming Language

Python

Related Categories

Python Bio-Informatics Software

Registered

2013-12-09