ModuleAlign – Module-based Global Alignment of Protein-protein Interaction networks

ModuleAlign

:: DESCRIPTION

ModuleAlign uses a novel scoring scheme that integrates sequence information and both local and global network topology. It computes a homology score between proteins based on a hierarchical clustering of the input networks. (a) shows the hierarchical structure of a network. Leaves represent the proteins and each cluster joins sets of proteins with similar interactions.

::DEVELOPER

Somaye Hashemifar

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux

:: DOWNLOAD

ModuleAlign

:: MORE INFORMATION

Citation:

Hashemifar S, Ma J, Naveed H, Canzar S, Xu J.
ModuleAlign: module-based global alignment of protein-protein interaction networks.
Bioinformatics. 2016 Sep 1;32(17):i658-i664. doi: 10.1093/bioinformatics/btw447. PMID: 27587686.

ConvexAlign – Find Global Alignment between Multiple of networks

ConvexAlign

:: DESCRIPTION

ConvexAlign finds a global alignment between multiple input PPI networks by convex optimization of a scoring function composed of sequence similarity, topological score, and interaction conservation score.

::DEVELOPER

Somaye Hashemifar

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux / Windows
Matlab

:: DOWNLOAD

ConvexAlign

:: MORE INFORMATION

Citation:

Hashemifar S, Huang Q, Xu J.
Joint Alignment of Multiple Protein-Protein Interaction Networks via Convex Optimization.
J Comput Biol. 2016 Nov;23(11):903-911. doi: 10.1089/cmb.2016.0025. Epub 2016 Jul 18. PMID: 27428933.

IsoRank 2008 / IsoRankN 2009 – Global Alignment of multiple PPI Networks / on Spectral methods

IsoRank 2008 / IsoRankN 2009

:: DESCRIPTION

IsoRank is an algorithm for global alignment of multiple protein-protein interaction (PPI) networks. The intuition is that a protein in one PPI network is a good match for a protein in another network if the former’s neighbors are good matches for the latter’s neighbors.

IsoRankN (IsoRank-Nibble) is a global multiple-network alignment tool based on spectral clustering on the induced graph of pairwise alignment scores. IsoRankN outperforms existing algorithms for global network alignment in coverage and consistency on multiple alignments of the five available eukaryotic networks.

::DEVELOPER

Bonnie Berger‘s group at MIT.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux

:: DOWNLOAD

IsoRank / IsoRankN

:: MORE INFORMATION

Citation:

Global alignment of multiple protein interaction networks with application to functional orthology detection.
Singh R, Xu J, Berger B.
Proc Natl Acad Sci U S A. 2008 Sep 2;105(35):12763-8. doi: 10.1073/pnas.0806627105.

IsoRankN: spectral methods for global alignment of multiple protein networks.
Liao CS, Lu K, Baym M, Singh R, Berger B.
Bioinformatics. 2009 Jun 15;25(12):i253-8. doi: 10.1093/bioinformatics/btp203.

MAPGAPS 1.0.1 – Multiply-Aligned Profiles for Global Alignment of Protein Sequences

MAPGAPS 1.0.1

:: DESCRIPTION

The MAPGAPS program uses a set of multiply-aligned profiles both as a query to detect and classify related sequences and as a template to multiply-align the sequences.

::DEVELOPER

Andrew F. Neuwald, Ph.D.

:: REQUIREMENTS

Linux

:: DOWNLOAD

MAPGAPS

:: MORE INFORMATION

Citation

Bioinformatics. 2009 Aug 1;25(15):1869-75. doi: 10.1093/bioinformatics/btp342. Epub 2009 Jun 8.
Rapid detection, classification and accurate alignment of up to a million or more related protein sequences.
Neuwald AF

GAST – Global Alignment for Sequence Taxonomy

GAST

:: DESCRIPTION

The GAST algorithm assigns taxonomy to SSU sequences by comparing them to a set of reference sequences with known taxonomy. In the simplest terms, taxonomy is assigned to each query sequence based on the consensus of the nearest references sequences. The alignment distance between the query and references is also reported as a measure of how similar the query and reference sequences really are.

::DEVELOPER

The VAMPS project

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux
Perl

:: DOWNLOAD

GAST

:: MORE INFORMATION

Citation:

Huse SM, Dethlefsen L, Huber JA, Mark Welch D, Relman DA, et al. (2008)
Exploring Microbial Diversity and Taxonomy Using SSU rRNA Hypervariable Tag Sequencing.
PLoS Genetics 4: e1000255..