Tag: Similarity

NaviGO – An analytic tool for Gene Ontology Visualization and Similarity

NaviGO

:: DESCRIPTION

NaviGO is a web-based tool for interactive visualization, retrieval, and computation of functional similarity and associations of GO terms and genes.

::DEVELOPER

Kihara Bioinformatics Laboratory

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

NaviGO: interactive tool for visualization and functional similarity and coherence analysis with gene ontology.
Wei Q, Khan IK, Ding Z, Yerneni S, Kihara D.
BMC Bioinformatics. 2017 Mar 20;18(1):177. doi: 10.1186/s12859-017-1600-5.

EFI-EST – Generating Protein Sequence Similarity Networks

EFI-EST

:: DESCRIPTION

EFI-EST (Enzyme Function Initiative-Enzyme Similarity Tool) web tool  is available without cost for the automated generation of protein sequence similarity networks.

::DEVELOPER

EFI-EST team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • web browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation:

Enzyme Function Initiative-Enzyme Similarity Tool (EFI-EST): A web tool for generating protein sequence similarity networks.
Gerlt JA, Bouvier JT, Davidson DB, Imker HJ, Sadkhin B, Slater DR, Whalen KL.
Biochim Biophys Acta. 2015 Apr 18. pii: S1570-9639(15)00112-0. doi: 10.1016/j.bbapap.2015.04.015.

Rchemcpp 2.24.0 – An R package for Computing the Similarity of Molecules

Rchemcpp 2.24.0

:: DESCRIPTION

Chemcpp is an R package that is the computation of similarities between molecules by kernel functions.

::DEVELOPER

Institute of Bioinformatics, Johannes Kepler University Linz

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/ Linux / MacOsX
  • R
  • BioConductor

:: DOWNLOAD

Rchemcpp

:: MORE INFORMATION

Citation

Rchemcpp: a web service for structural analoging in ChEMBL, Drugbank and the Connectivity Map.
Klambauer G, Wischenbart M, Mahr M, Unterthiner T, Mayr A, Hochreiter S.
Bioinformatics. 2015 Oct 15;31(20):3392-4. doi: 10.1093/bioinformatics/btv373.

MCQ4Structures 1.6.1 – Computing Similarity of 3D RNA / Protein Structures

MCQ4Structures 1.6.1

:: DESCRIPTION

MCQ4Structures is a tool for structural similarity computation based on molecule tertiary structure representation in torsional angle space. Although it has been primarily designed to work with RNA structures, MCQ4Structures can be also applied to proteins (however their representation is restricted to the backbone angles).

::DEVELOPER

Tomasz Żok

:: SCREENSHOTS

MCQ4Structures

:: REQUIREMENTS

  • Windows/ Linux /MacOsX
  • Java

:: DOWNLOAD

 MCQ4Structures

:: MORE INFORMATION

Citation

BMC Bioinformatics. 2017 Oct 23;18(1):456. doi: 10.1186/s12859-017-1867-6.
LCS-TA to identify similar fragments in RNA 3D structures.
Wiedemann J, Zok T, Milostan M, Szachniuk M

UniDPlot 1.2.2 – Detect Weak Similarities between two DNA sequences

UniDPlot 1.2.2

:: DESCRIPTION

UniDPlot is designed to easily search for short sequences in large genomic contig.

::DEVELOPER

Marc Girondot   & Jean-Yves Sire

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows/ MacOs

:: DOWNLOAD

 UniDPlot

:: MORE INFORMATION

Citation

Girondot, M. and J.-Y. Sire 2010.
UniDPlot : A software to detect weak similarities between two DNA sequences.
Journal of Bioinformatics and Sequence Analysis 2(5): 69-74.

NPUTE – Data Structure for Finding Pair-wise Haplotype Similarity

NPUTE

:: DESCRIPTION

NPUTE is an efficient data structure we have developed for finding pair-wise haplotype similarity. Its simplicity can lead to benefits in speed and exhaustive searches over multiple parameters.

::DEVELOPER

the UNC Computational Genetics Working Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 NPUTE

:: MORE INFORMATION

SimTree 1.2.3 – Compute Similarity between RNA Secondary Structure

SimTree 1.2.3

:: DESCRIPTION

SimTree is an online tool for computing the similarity between RNA secondary structures.

::DEVELOPER

Eran Eden , Izhar Wallach (izharw@keddem.com) ,Zohar Yakhini @ Laboratory of Computational Biology , Technion

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/windows/MacOsX
  • Java
  • Web Server

:: DOWNLOAD

 SimTree

:: MORE INFORMATION

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