TreeDom – Flexible tool for Analysing Protein Domain Architecture Evolution

TreeDom

:: DESCRIPTION

TreeDom is a flexible tool for analysing protein domain architecture evolution.

:: DEVELOPER

Sonnhammer Bioinformatics Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

  NO

:: MORE INFORMATION

Citation

Bioinformatics. 2016 Aug 1;32(15):2384-5. doi: 10.1093/bioinformatics/btw140.
TreeDom: a graphical web tool for analysing domain architecture evolution.
Haider C, Kavic M, Sonnhammer EL.

DPUC 2.08 – Using Context to Improve Protein Domain Identification

DPUC 2.08

:: DESCRIPTION

DPUC (Domain Prediction Using Context) extends your Pfam predictions without loss of precision using domain context!

::DEVELOPER

The Ochoa Lab 

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 DPUC

:: MORE INFORMATION

Citation

BMC Bioinformatics. 2011 Mar 31;12:90. doi: 10.1186/1471-2105-12-90.
Using context to improve protein domain identification.
Ochoa A1, Llinás M, Singh M.

DomStratStats – Compute per-protein Domain Family q-values and local FDRs

DomStratStats

:: DESCRIPTION

DomStratStats computes domain q-values and local FDRs, and tiered q-values (combining HMMER3 domain and sequence data).

::DEVELOPER

Mona Singh

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ MacOsX
  • Perl

:: DOWNLOAD

DomStratStats

:: MORE INFORMATION

Citation

PLoS Comput Biol. 2015 Nov 17;11(11):e1004509. doi: 10.1371/journal.pcbi.1004509. eCollection 2015 Nov.
Beyond the E-Value: Stratified Statistics for Protein Domain Prediction.
Ochoa A, Storey JD, Llinás M, Singh M.

dcGOR 1.0.6 – Analysing Ontologies and Protein Domain Annotations

dcGOR 1.0.6

:: DESCRIPTION

dcGOR is an open-source R package for analysing domain-centric ontologies and annotations  (dcGO and others)

::DEVELOPER

Dr. Hai Fang

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows/ MacOsX
  • R

:: DOWNLOAD

 dcGOR

:: MORE INFORMATION

Citation:

PLoS Comput Biol. 2014 Oct 30;10(10):e1003929. doi: 10.1371/journal.pcbi.1003929. eCollection 2014.
dcGOR: an R package for analysing ontologies and protein domain annotations.
Fang H

T-RMSD – Allows fine-grained Structural Clustering of a given group of related Protein Domains

T-RMSD

:: DESCRIPTION

T-RMSD web server (tree-based on root-mean-square deviation) is a service allowing the online computation of structure-based protein classification.

::DEVELOPER

Notredame’s Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation:

T-RMSD: a web server for automated fine-grained protein structural classification.
Magis C, Di Tommaso P, Notredame C.
Nucleic Acids Res. 2013 Jul;41(Web Server issue):W358-62. doi: 10.1093/nar/gkt383.

DomEx – Extending Protein Domain Boundary Predictors

DomEx

:: DESCRIPTION

DomEx is an Extending Protein domain predictors to detect discontinuous domains

::DEVELOPER

zhidong xue (zdxue@hust.edu.cn)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows
  • Perl

:: DOWNLOAD

 DomEx

:: MORE INFORMATION

Citation

Extending Protein Domain Boundary Predictors to Detect Discontinuous Domains.
Xue Z, Jang R, Govindarajoo B, Huang Y, Wang Y.
PLoS One. 2015 Oct 26;10(10):e0141541. doi: 10.1371/journal.pone.0141541.

DAMA – Protein Domain Architectures

DAMA

:: DESCRIPTION

DAMA (Domain Annotation by a Multi-objective Approach) is a novel approach that identifies architectures through a multi-objective optimisation algorithm combining scores of domain matches, previously observed multi-domain co-occurrence, and domain overlapping.

::DEVELOPER

Laboratory of Computational and Quantitative Biology(LCQB)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • C++ Compiler

:: DOWNLOAD

 DAMA

:: MORE INFORMATION

Citation

A multi-objective optimisation approach accurately resolves protein domain architectures.
Bernardes JS, Vieira FR, Zaverucha G, Carbone A.
Bioinformatics. 2015 Oct 12. pii: btv582.

d-Omix – Mixer of Protein Domain Analysis Tools

d-Omix

:: DESCRIPTION

d-Omix is a web server aiming as a unified platform to analyze, compare, and visualize protein data sets in various aspects of protein domain combinations.

::DEVELOPER

Information Systems Laboratory at BIOTEC

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Nucleic Acids Res. 2009 Jul;37(Web Server issue):W417-21. doi: 10.1093/nar/gkp329. Epub 2009 May 21.
d-Omix: a mixer of generic protein domain analysis tools.
Wichadakul D1, Numnark S, Ingsriswang S.

DoBo – Protein Domain Boundary Prediction by integrating Evolutionary Signals and Machine Learning

DoBo

:: DESCRIPTION

DoBo (Domain Boundary) is a tool to identify domain boundaries from sequence. It works by combining the classification power of machine learning with domain boundary signals embedded in multiple sequence alignments.

::DEVELOPER

MLiD Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

NO

:: MORE INFORMATION

Citation

BMC Bioinformatics. 2011 Feb 1;12:43. doi: 10.1186/1471-2105-12-43.
DoBo: Protein domain boundary prediction by integrating evolutionary signals and machine learning.
Eickholt J1, Deng X, Cheng J.

PDART – Protein Domain Architecture Retrieval Tool

PDART

:: DESCRIPTION

PDART is a web site to compare domain architectures or proteins.

:: DEVELOPER

Laboratory of Computational Molecular Biology, Beijing Normal University.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • WEb browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Bioinformatics. 2006 Sep 1;22(17):2081-6. Epub 2006 Jul 12.
An initial strategy for comparing proteins at the domain architecture level.
Lin K1, Zhu L, Zhang DY.