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PISwap specifications

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Unique identifier OMICS_04882
Name PISwap
Software type Package/Module
Interface Command line interface
Restrictions to use Academic or non-commercial use
Operating system Unix/Linux
Programming languages Python
Computer skills Advanced
Stability Stable
Maintained Yes

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Publication for PISwap

PISwap citations

 (2)
call_split

Unified Alignment of Protein Protein Interaction Networks

2017
Sci Rep
PMCID: 5430463
PMID: 28424527
DOI: 10.1038/s41598-017-01085-9
call_split See protocol

[…] ming the first pass and then simply performing a maximum-weight bipartite matching, whereas Mode 2 performs the two passes. On our datasets, only Mode 1 returned alignments for all PPI network pairs. PISWAP first identifies an optimal global alignment based purely on sequence data. Then, it uses the intuition that biologically conserved interactions can compensate for mapping proteins whose seque […]

library_books

Scalable global alignment for multiple biological networks

2012
BMC Bioinformatics
PMCID: 3311098
PMID: 22536895
DOI: 10.1186/1471-2105-13-S3-S11

[…] nt for large networks, but if the legal matches are all pairs of proteins across two networks, as in the general (unconstrained) network alignment problem, they both suffer from a large space demand. PISwap first utilizes the Hungarian algorithm [], which is used to find the global matches which maximize the similarity score, and then use a method similar to 2-0pt [], which is a heuristic algorith […]


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PISwap institution(s)
Computer Science and Artificial Intelligence Laboratory and Department of Mathematics, Massachusetts Institute of Technology, Cambridge, MA, USA; Department of Computer Science and Department of Industrial Engineering and Engineering Management, National Tsing Hua University, Hsinchu, Taiwan

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