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Network querying software tools | Systems biology

Network querying algorithms provide computational means to identify conserved network modules in large-scale biological networks that are similar to known functional modules, such as pathways or molecular complexes. Two main challenges for network…
NetMatch
Desktop

NetMatch

Allows to find all the occurrences of a query graph in a network and check for…

Allows to find all the occurrences of a query graph in a network and check for its significance as a motif with respect to seven different random models. NetMatch offers the ability to compute a…

TORQUE
Web

TORQUE TOpology-free netwoRk QUErying

Allows network querying that does not rely on knowledge of the query topology.…

Allows network querying that does not rely on knowledge of the query topology. TORQUE uses as input a set of proteins from a source species in the protein protein interaction (PPI) network of a…

MetaPathwayHunt…
Desktop

MetaPathwayHunter

Permits pathway alignments. MetaPathwayHunter is based on an approximate…

Permits pathway alignments. MetaPathwayHunter is based on an approximate pattern matching algorithm for labeled graphs. It was used to build a study on the similarities and variations in the…

QPath
Algorithm

QPath

Allows querying linear pathways within a given network. QPath searches for…

Allows querying linear pathways within a given network. QPath searches for matching pathways composed of distinct proteins that are similar to the query proteins in their sequence and interaction…

Significance…
Desktop

Significance Enhanced QUerying Of InterAction networks

Identifies conserved subnetwork regions in the target network that are similar…

Identifies conserved subnetwork regions in the target network that are similar to a given query network. SEQUOIA is a network querying algorithm that compares two networks and estimates the node…

RESQUE
Desktop

RESQUE REduction-based scheme using Semi-Markov scores for network QUErying

Allows network querying. RESQUE takes a reduction-based approach, where the…

Allows network querying. RESQUE takes a reduction-based approach, where the target network is iteratively reduced based on the so-called node correspondence scores that are computed using a…

CNetQ
Web

CNetQ Conditional Random Fields based Network Querying Method

Represents a method for network querying problem. CNetQ allows users to find…

Represents a method for network querying problem. CNetQ allows users to find the conserved functionally similar modules and pathways in both undirected and directed biomolecular networks. This method…

QNet
Algorithm

QNet

Permits tree queries. QNet can handle queries of up to nine proteins in seconds…

Permits tree queries. QNet can handle queries of up to nine proteins in seconds in a network with about 5000 vertices and 15,000 interactions. It is able to perform a large-scale cross-species…

Corbi
Desktop

Corbi

Provides several tools for bioinformatics analysis. Corbi is an R package that…

Provides several tools for bioinformatics analysis. Corbi is an R package that contains functions for network querying and alignment, subnetwork extraction, search and biomarker identification. The…

PathBLAST
Web

PathBLAST

A network alignment and search tool for comparing protein interaction networks…

A network alignment and search tool for comparing protein interaction networks across species to identify protein pathways and complexes that have been conserved by evolution. The basic method…

RINQ
Algorithm

RINQ Reference-based Indexing for Biological Network Queries

Answers similarity queries in biological network databases. RINQ is a…

Answers similarity queries in biological network databases. RINQ is a reference-based indexing method whose main advantage is its independence of the pairwise network alignment algorithm the database…

SAGA
Desktop

SAGA Substructure Index-based Approximate Graph Alignment

A tool for querying a biological graph database to retrieve matches between…

A tool for querying a biological graph database to retrieve matches between subgraphs of molecular interactions and biological networks. SAGA implements an efficient approximate subgraph matching…

NatalieQ
Web

NatalieQ

Molecular interactions need to be taken into account to adequately model the…

Molecular interactions need to be taken into account to adequately model the complex behavior of biological systems. NatalieQ is a web server for aligning two protein-interaction networks in order to…

MaWISh
Desktop

MaWISh Maximum Weight Induced Subgraph

A comprehensive alignment tool for PPI networks, which is inspired by…

A comprehensive alignment tool for PPI networks, which is inspired by duplication/divergence models that focus on understanding the evolution of protein interactions. MaWISh is based on a…

APPAGATO
Desktop

APPAGATO APproximate PArallel and stochastic GrAph querying Tool

Finds approximate occurrences of a query network in biological networks.…

Finds approximate occurrences of a query network in biological networks. APPAGATO handles node, edge and node label mismatches. It applies to large networks and provides high performance as well as…

AbiNet
Web

AbiNet

Allows users to align and query biological networks. AbiNet matches connected…

Allows users to align and query biological networks. AbiNet matches connected subgraphs to proceed. It constructs a one-to-one correspondence between pairs of nodes in the two networks. This tool can…

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