TORQUE – Topology-Free Querying of Protein Interaction Networks

TORQUE

:: DESCRIPTION

TORQUE is a tool for cross-species querying of protein-protein interaction networks. Given a complex (set of proteins) for a query species, Torque seeks a matching set of proteins of a target species that are sequence-similar to the query proteins and span a connected region of the target network.

::DEVELOPER

Ron Shamir’s lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

TORQUE: topology-free querying of protein interaction networks.
Bruckner S, Hüffner F, Karp RM, Shamir R, Sharan R.
Nucleic Acids Res. 2009 Jul;37(Web Server issue):W106-8. doi: 10.1093/nar/gkp474.

NatalieQ – Topology-based Protein-protein Interaction Network Querying

NatalieQ

:: DESCRIPTION

NatalieQ is a web server for aligning two protein-interaction networks in order to highlight conserved subnetworks. It is an interface to the more general network alignment method Natalie.

::DEVELOPER

The Centre for Integrative Bioinformatics VU

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

BMC Syst Biol. 2014 Apr 1;8:40. doi: 10.1186/1752-0509-8-40.
NatalieQ: a web server for protein-protein interaction network querying.
El-Kebir M, Brandt BW, Heringa J, Klau GW.

GenoQuery – Querying Genomic Data Warehouse

GenoQuery

:: DESCRIPTION

GenoQuery is a module for querying a relational genomic warehouse, which is based on an original multi-layer architecture of the warehouse, made of two layers, the entities layer and the databases layer.

::DEVELOPER

Christine Froidevaux

:: SCREENSHOTS

GenoQuery

:: REQUIREMENTS

  • Windows/Linux/MacOsX
  • Java

:: DOWNLOAD

 GenoQuery

:: MORE INFORMATION

Citation

Frederic Lemoine, Bernard Labedan, Christine Froidevaux
GenoQuery: a new querying module for functional annotation in a genomic warehouse
Bioinformatics (ISMB 2008), 07, 13, i322-i329, 24, 2008

Kafeen 2.1.0 – Querying Genetic Variation data from database

Kafeen 2.1.0

:: DESCRIPTION

Kafeen is a quick and easy command-line tool for locally querying genetic variation data from dbNSFP, ESP6500SI, 1000 Genomes, and OtoSCOPE. Its output is configurable and is meant to be tailored to your own local database needs.

::DEVELOPER

Coordinated Laboratory for Computational Genomics (CLCG)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/MacOsX
  • Ruby
  • Java

:: DOWNLOAD

 Kafeen 

:: MORE INFORMATION

Cyclone 1.0 beta – Java-based Querying and Computing with Pathway/Genome databases

Cyclone 1.0 beta

:: DESCRIPTION

Cyclone aims at facilitating the use of BioCyc, a biological pathway tool. Cyclone provides a comprehensive library of Java classes.

::DEVELOPER

Genoscope – Institut de Génomique – CEA

:: SCREENSHOTS

Cyclone

:: REQUIREMENTS

  • Windows/Linux/MacOsX
  • Java

:: DOWNLOAD

 Cyclone

:: MORE INFORMATION

Citation

Bioinformatics. 2007 May 15;23(10):1299-300. Epub 2007 Mar 28.
Cyclone: java-based querying and computing with Pathway/Genome databases.
Le Fèvre F1, Smidtas S, Sch?chter V.

RESQUE 1.0 – REduction-based scheme using Semi-Markov scores for networkQUEing

RESQUE 1.0

:: DESCRIPTION

RESQUE is an efficient algorithm for querying large-scale biological networks.

::DEVELOPER

Mohammad Ebrahim Sahraeian and Byung-Jun Yoon

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ Windows/ MacOsX
  • Python / Matlab

:: DOWNLOAD

 RRESQUE

:: MORE INFORMATION

Citation

RESQUE: Network reduction using semi-Markov random walk scores for efficient querying of biological networks
Sayed Mohammad Ebrahim Sahraeian and Byung-Jun Yoon,
Bioinformatics, 28 (16): 2129-2136, 2012. doi:10.1093/bioinformatics/bts341

GQL 1.0 – GHMM-based tool for Querying and Clustering Gene-Expression time-course data

GQL 1.0

:: DESCRIPTION

GQL (Graphical Query Language) is a suite of tools for analyizing time-course experiments. Currently, it is adapted to gene expression data. The two main tools are GQLQuery, for querying data sets, and GQLCluster, which provides a way for computing groupings based on a number of methods (model-based clustering using HMMs as cluster models and estimation of a mixture of HMMs).

::DEVELOPER

Alexander Schliep’s group for bioinformatics

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 GQL

:: MORE INFORMATION

Citation

Bioinformatics. 2005 May 15;21(10):2544-5. Epub 2005 Feb 8.
The Graphical Query Language: a tool for analysis of gene expression time-courses.
Costa IG, Schönhuth A, Schliep A.