MAGNA++ 20150130 – Maximizing Accuracy in Global Network Alignment

MAGNA++20150130

:: DESCRIPTION

MAGNA++ is a software tool for pairwise global network alignment. It is an extension of MAGNA. An example of an application domain where MAGNA++ is useful is computational biology – MAGNA++ can be used for biological network alignment.

MAGNA is an network alignment algorithm. MAGNA is a pairwise global aligner and a genetic algorithm. It can either start computation from precomputed alignments,or start completely from scratch.

::DEVELOPER

Complex Networks (CoNe) Lab

:: SCREENSHOTS

:: REQUIREMENTS

Linux / Windows / MacOsX

:: DOWNLOAD

MAGNA

:: MORE INFORMATION

Citation:

MAGNA++: Maximizing Accuracy in Global Network Alignment via both node and edge conservation.
Vijayan V, Saraph V, Milenković T.
Bioinformatics. 2015 Mar 19. pii: btv161

MAGNA: Maximizing Accuracy in Global Network Alignment.
Saraph V, Milenkovic T.
Bioinformatics. 2014 Jul 10. pii: btu409.

AlignNemo 1.1 – Local Network Alignment method to integrate Homology and Topology

AlignNemo 1.1

:: DESCRIPTION

AlignNemo (Aligning Network Modules), is a novel algorithm that, given the networks of two organisms, uncovers subnetworks of proteins that related in sequence and topology. The subnetworks have a general topology and need not to correspond to specific interaction patterns thus more closely fit the models of functional complexes proposed in the literature.

::DEVELOPER

AlignNemo Team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Windows / Mac / Linux
Java

:: DOWNLOAD

AlignNemo

:: MORE INFORMATION

Citation

PLoS One. 2012;7(6):e38107. Epub 2012 Jun 12.
AlignNemo: a local network alignment method to integrate homology and topology.
Ciriello G, Mina M, Guzzi PH, Cannataro M, Guerra C.

NAPAbench 1.0 – Network Alignment Performance Assessment Benchmark

NAPAbench 1.0

:: DESCRIPTION

NAPAbench is a large-scale network alignment benchmark which evaluated the performance of several representative network alignment algorithms.

::DEVELOPER

Mohammad Ebrahim Sahraeian and Byung-Jun Yoon

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux

:: DOWNLOAD

NAPAbench

:: MORE INFORMATION

Citation

A Network Synthesis Model for Generating Protein Interaction Network Families
Sayed Mohammad Ebrahim Sahraeian and Byung-Jun Yoon,
PLoS One, 7(8): e41474, 2012. doi:10.1371/journal.pone.0041474

SMETANA 1.0 – Semi-Markov random walk scores Enhanced by consistency Transformation for Accurate Network Alignment

SMETANA 1.0

:: DESCRIPTION

SMETANA is an efficient algorithm for alignment of multiple large-scale biological networks.SMETANA can easily align tens of genome-scale networks with thousands of nodes on a personal computer.

::DEVELOPER

Mohammad Ebrahim Sahraeian and Byung-Jun Yoon

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux

:: DOWNLOAD

SMETANA

:: MORE INFORMATION

Citation

SMETANA: Accurate and Scalable Algorithm for Probabilistic Alignment of Large-Scale Biological Networks
Sayed Mohammad Ebrahim Sahraeian and Byung-Jun Yoon,
PLoS One, 8(7): e67995, 2013. doi:10.1371/journal.pone.0067995