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BP_Prior v2.9.1 (a.k.a. PERA)

posted on 10.01.2015, 16:20 by B. Arman AksoyB. Arman Aksoy, Emek Demir, Özgün Babur, Anil Korkut, Chris Sander

BioPAX (BP) Prior (also known as PERA) is a tool for people who work with proteomics data and want to conduct pathway-context aware analysis. Given a set of annotated protein states, (such as phosphorylations, active/inactive tags and concentration levels), this programs creates a map from the input states onto the Pathway Commons 2 entities and finds the minimum distance between them -- the distances are extracted from BioPAX graphs. The ouput, so called prior information network, is a tab-limited file in Simple Interaction Format and it contains:

- Source/target entities

- Directional distance measure between these two entities

- Pubmed IDs associated with links as external references

- Reactions and their types included in the path between two entities.


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