Tag: Construct

Assemble2 2.3 – Construct & Study RNA Architectures

Assemble2 2.3

:: DESCRIPTION

Assemble proposes an intuitive graphical interface to study and construct complex three-dimensional RNA structures. When an RNA tertiary structure is opened with Assemble, it is automatically annotated with a secondary structure definition. This secondary structure can be used as a map to analyze the original tertiary structure. Using a secondary structure definition, Assemble can also produce a first draft of a 3D Model. Then the construction process can be pursued “by hand” using several widgets.

::DEVELOPER

Dr. Fabrice Jossinet at the laboratory of Pr. Eric Westhof

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / MacOsX / Linux
  • Java

:: DOWNLOAD

Assemble

:: MORE INFORMATION

Citation

Assemble: an interactive graphical tool to analyze and build RNA architectures at the 2D and 3D levels
Fabrice Jossinet; Thomas E Ludwig; Eric Westhof
Bioinformatics 2010; doi: 10.1093/bioinformatics/btq321

conStruct v1.0.3 – Modeling Continuous and Discrete Population Genetic Structure

conStruct v1.0.3

:: DESCRIPTION

conStruct (continuous Structure) is a statistical tool for modeling continuous and discrete population genetic structure.

::DEVELOPER

the Bradburd Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux / MacOS
  • R package

:: DOWNLOAD

conStruct

:: MORE INFORMATION

Citation

Bradburd GS, Coop GM, Ralph PL.
Inferring Continuous and Discrete Population Genetic Structure Across Space.
Genetics. 2018 Sep;210(1):33-52. doi: 10.1534/genetics.118.301333. Epub 2018 Jul 19. PMID: 30026187; PMCID: PMC6116973.

RFsupertrees 2.0 – Program for Constructing Accurate Supertrees

RFsupertrees 2.0

:: DESCRIPTION

RFsupertrees (Robinson-Foulds Supertrees) takes as input a collection of rooted trees and heuristically searches for a binary supertree that minimizes the total (rooted) Robinson-Foulds distance between the supertree and the input trees. The intuition behind seeking a binary supertree, even though the input trees may be non-binary (unresolved), is that, under this setting, minimizing the RF distance is equivalent to maximizing the number of shared clades (or clusters) between the input trees and the supertree. Thus, an RF supertree is a supertree that is consistent with the largest number of clusters from the input trees. The program can quickly compute accurate supertrees for even large datasets containing thousands of input trees with many hundreds of taxa.

::DEVELOPER

Computational Biology Laboratory, Department of Computer Science,Iowa State University

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux / Mac OsX

:: DOWNLOAD

 RFsupertrees

:: MORE INFORMATION

Citation

Robinson-Foulds Supertrees
Mukul S. Bansal, J. G. Burleigh, Oliver Eulenstein, David Fernandez-Baca.
Algorithms for Molecular Biology 2010, 5:18.

Cri-Map 2.4 – Construct Multilocus Linkage Map

Cri-Map 2.4

:: DESCRIPTION

CRI-MAP‘s purpose is to allow rapid, largely automated construction of multilocus linkage maps (and facilitate the attendant tasks of assessing support relative to alternative locus orders, generating LOD tables, and detecting data errors). Although originally designed to handle codominant loci (e.g. RFLPs) scored on pedigrees “without missing individuals”, such as CEPH or nuclear families, it can now (with some caveats described below) be used on general pedigrees, and some disease loci.

::DEVELOPER

Matise Laboratory of Computational Genetics.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows wity Cygwin /MacOsX
  • GCC
:: DOWNLOAD

  CRI-MAP

:: MORE INFORMATION

Citation

Hum Hered. 1995 Mar-Apr;45(2):103-16.
Parallel computation of genetic likelihoods using CRI-MAP, PVM, and a network of distributed workstations.
Matise TC, Schroeder MD, Chiarulli DM, Weeks DE.

RNAlocmin 2.1 – Finds local Minima of RNA + Constructs Barrier Tree

RNAlocmin 2.1

:: DESCRIPTION

The program RNAlocmin reads secondary structures to RNA sequence provided in file seq.txt (can be altered with “-s” option) and search for a local minima by performing a gradient walk.

::DEVELOPER

Theoretical Biochemistry Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • ViennaRNA

:: DOWNLOAD

 RNAlocmin

:: MORE INFORMATION

OpenGrowth 1.0.1 – Construct de novo Ligands for Protein

OpenGrowth 1.0.1

:: DESCRIPTION

OpenGrowth is a research program which grows new ligands in proteins by connecting small organic fragments.

::DEVELOPER

The Shakhnovich Biophysics Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • MacOsX / Linux

:: DOWNLOAD

 OpenGrowth

:: MORE INFORMATION

Citation

OpenGrowth: An Automated and Rational Algorithm for Finding New Protein Ligands.
Chéron N, Jasty N, Shakhnovich EI.
J Med Chem. 2015 Sep 23

E-RNAi 3.2 – Design Optimized RNAi Constructs

E-RNAi 3.2

:: DESCRIPTION

E-RNAi is a tool for the design and evaluation of RNAi reagents for a variety of species. It can be used to design and evaluate long dsRNAs (including esiRNAs) as well as siRNAs.

::DEVELOPER

E-RNAi team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser 

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

E-RNAi: a web application for the multi-species design of RNAi reagents–2010 update.
Thomas Horn; Michael Boutros
Nucl. Acids Res. (2010) 38 (suppl 2): W332-W339. doi: 10.1093/nar/gkq317

REMO 2.0 – Construct Full-atom Protein Models from C-alpha Traces

REMO 2.0

 

:: DESCRIPTION

REMO is a multifunctional program for constructing full-atom protein models from C-alpha traces by optimizing the backbone hydrogen-bonding networks. It gives options to choose models which are close to a given template or have more hydrogen-bonds. It has also options to build hydrogen atoms and side chain heavy atoms. The bond length and bond angle parameters are taken from CHARMM22.

::DEVELOPER

Yang Zhang’s Research Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows / Mac OsX
  • Perl

:: DOWNLOAD

 REMO

:: MORE INFORMATION

Citation

Yunqi Li and Yang Zhang.
REMO: A new protocol to refine full atomic protein models from C-alpha traces by optimizing hydrogen-bonding networks.
Proteins, 2009, 76: 665-676

Clann 4.2.5 – Construct Phylogenetic Supertrees

Clann 4.2.5

:: DESCRIPTION

Clann (the Irish word for “family”), is a free software program designed and written by Chris Creevey at the Bioinformatics and Pharmacogenomics Laboratory at NUI Maynooth. The purpose of the program is to implement methods of determining the optimal phylogenetic supertree, given a set of input source trees.

::DEVELOPER

McInerney lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux / MacOS

:: DOWNLOAD

Clann

:: MORE INFORMATION

Citation:

Creevey C. J. and McInerney, J. O. 2005
Clann: Investigating phylogenetic information through supertree analyses.
Bioinformatics 21 (3): 390-2.

Graph 1.0 – Constructs, Visualizes and Modifies Graphs

Graph 1.0

:: DESCRIPTION

Graph constructs, visualizes and modifies graphs as well as calculates measures and layouts

::DEVELOPER

The Microsoft Research – University of Trento Centre for Computational and Systems Biology

:: SCREENSHOTS

Graph

:: REQUIREMENTS

  • Windows
  • .NET Framework

:: DOWNLOAD

 Graph

:: MORE INFORMATION

Citation

Roberto Valentini, Ferenc Jordan.
COSBILab Graph: the network analysis module of COSBILab Environmental Modelling and Software, 25:886-888, 2010