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PcPipe 1.0.0

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PcPipe is a pipeline that implements a series of steps for protein clustering and annotation. 1: User defined proteins are clustered with proteins from known protein clusters. 2: Proteins that do not cluster are self-clustered to form novel protein clusters. 3: Proteins from novel self-clusters are compared to a reference set of proteins from the Similarity Matrix of Proteins (SIMAP). 4: Annotations from SIMAP proteins are assigned to each hit from the novel protein clusters.

Quick Start

• To use PcPipe 1.0.0, import your data in ___ format.
• Resources: http://replace.with.URL.for.tool.documentation.from.the.tool.source.org

Test Data

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• PCPipe

  Description and Quick Start

  Protein clustering

  Test Data

  /iplant/home/shared/imicrobe/pcpipe

  Input File(s)

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• Protein clustering.

  Parameters Used in App

When the app is run in the Discovery Environment, use the following parameters with the above input file(s) to get the output provided in the next section below.

Use either the "Default parameters..." section OR fill in the "Use these parameters..." section. Delete the unused section and the OR. Then, delete this note.

• Default parameters only, no further configuration needed.

OR

• Use these parameters within the DE app interface:
• parameter name - value/setting
parameter name - value/setting

ORFs and existing protein clusters.

Output File(s)

Expect a text file named after the input files as output. For the test case, the output file you will find in the example_data directory is named BeautifulProse.txt.

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• BLAST results annotated with SIMAP features.

• Protocol for use is here: https://www.protocols.io/view/PCPipe-Protein-clustering-with-SIMAP-annotations-ehfbb3n

• https://github.com/hurwitzlab/pcpipe
• http://replacewww.with.URL.for.tool.orgnature.com/ismej/journal/vaop/ncurrent/full/ismej201689a.html?WT.feed_name=subjects_genetics