BNFinder 2.1.1 – Bayesian Network Topology Inference

BNFinder 2.1.1

:: DESCRIPTION

BNFinder (Bayesian Network Finder) allows for Bayesian network reconstruction from experimental data. It supports dynamic Bayesian networks and, if the variables are partially ordered, also static Bayesian networks.

::DEVELOPER

CompBio@MIMUW

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows/ MacOsX
  • Python

:: DOWNLOAD

 BNFinder

:: MORE INFORMATION

Citation

BNFinder2: Faster Bayesian network learning and Bayesian classification.
Dojer N, Bednarz P, Podsiadlo A, Wilczynski B.
Bioinformatics. 2013 Aug 15;29(16):2068-70. doi: 10.1093/bioinformatics/btt323.

Bioinformatics. 2009 Jan 15;25(2):286-7. doi: 10.1093/bioinformatics/btn505. Epub 2008 Sep 30.
BNFinder: exact and efficient method for learning Bayesian networks.
Wilczyński B, Dojer N.

MemPype – Pipeline for Predicting the Topology and the Localization of Membrane Proteins

MemPype

:: DESCRIPTION

MemPype is a Python-based pipeline that integrates several tools the prediction of topology and subcellular localization of Eukaryotic membrane proteins.

::DEVELOPER

Bologna Biocomputing Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 No. Only Web Service

:: MORE INFORMATION

Citation

Pierleoni A, Indio V, Savojardo C, Fariselli P, Martelli PL, Casadio R.
MemPype: a pipeline for the annotation of eukaryotic membrane proteins.
Nucl. Acids Res. (2011) 39 (suppl 2): W375-W380.

BetAware – Beta-Barrel Detection and Topology Prediction

BetAware

:: DESCRIPTION

BETAWARE is a software package designed for the analysis of trans-membrane beta-barrel proteins.

::DEVELOPER

Castrense Savojardo

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ MacOsX
  • Python
  • python argparse library
  • python numpy

:: DOWNLOAD

  BetAware

:: MORE INFORMATION

Citation

Bioinformatics. 2013 Feb 15;29(4):504-5. doi: 10.1093/bioinformatics/bts728. Epub 2013 Jan 6.
BETAWARE: a machine-learning tool to detect and predict transmembrane beta-barrel proteins in prokaryotes.
Savojardo C, Fariselli P, Casadio R.

FTALIGN – Fast Topology-independent and Global Structure Alignment through an FFT-based algorithm.

FTALIGN

:: DESCRIPTION

The FTALIGN server is to align two protein structures by using a fast Fourier transformation (FFT)-based topology-independent and global structure alignment algorithm.

::DEVELOPER

Huang Laboratary

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

FTALIGN

:: MORE INFORMATION

Citation:

Wen Z, He J, Huang SY.
Topology-independent and global protein structure alignment through an FFT-based algorithm.
Bioinformatics. 2020 Jan 15;36(2):478-486. doi: 10.1093/bioinformatics/btz609. PMID: 31384919.

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.

CCTOP 1.00 – Constrained Consensus TOPology prediction server

CCTOP 1.00

:: DESCRIPTION

CCTOP server is a web-based application providing transmembrane topology prediction.

::DEVELOPER

CCTOP team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

  CCTOP

:: MORE INFORMATION

Citation

CCTOP: a Consensus Constrained TOPology prediction web server.
Dobson L, Reményi I, Tusnády GE.
Nucleic Acids Res. 2015 May 5. pii: gkv451

JEPETTO 1.3.1 – Java Enrichment of Pathways Extended To Topology

JEPETTO 1.3.1

:: DESCRIPTION

JEPETTO is a Cytoscape 3.x plugin performing integrative human gene set analysis. It identifies functional associations between genes and known cellular pathways, and processes using protein interaction networks and topological analysis.

::DEVELOPER

Interdisciplinary Computing and Complex BioSystems (ICOS) research group

:: SCREENSHOTS

JEPETTO

:: REQUIREMENTS

  • Linux/ Windows/ MacOsX
  • Java
  • Cytoscape

:: DOWNLOAD

 JEPETTO

:: MORE INFORMATION

Citation:

Bioinformatics. 2014 Apr 1;30(7):1029-30. doi: 10.1093/bioinformatics/btt732. Epub 2013 Dec 19.
JEPETTO: a Cytoscape plugin for gene set enrichment and topological analysis based on interaction networks.
Winterhalter C1, Widera P, Krasnogor N.

MirrorT 0.1 – Mirroring Co-evolving Trees in Light of their Topologies

MirrorT 0.1

:: DESCRIPTION

MirrorT is a software of mirroring co-evolving trees in the light of their topologies

::DEVELOPER

Lab for Bioinformatics and Computational Genomics

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • C Complier

:: DOWNLOAD

 MirrorT

:: MORE INFORMATION

Citation

Mirroring co-evolving trees in the light of their topologies
Hajirasouliha I, Schonhuth A, de Juan D, Valencia A, Sahinalp SC
Bioinformatics. 2012 May 1;28(9):1202-8

simLoci 1.0 – Simulate Sequence data on an input Topology

simLoci 1.0

:: DESCRIPTION

The script simLoci.py can be used to simulate sequence data on an input topology under a coalescent model with arguments to allow migration between lineages and to modify population parameters.

::DEVELOPER

Deren Eaton

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ MacOsX / Windows
  • Python

:: DOWNLOAD

 simLoci

:: MORE INFORMATION

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