nFuse 0.2.1 – Discovery of Complex Genomic Rearrangements in Cancer

nFuse 0.2.1

:: DESCRIPTION

nFuse is a tool for detecting fusion transcripts and associated complex genomic rearrangements from matched RNA-seq and whole genome shotgun sequencing.nFuse predicts fusion transcripts and associated CGRs from matched RNA-seq and Whole Genome Shotgun Sequencing (WGSS).

::DEVELOPER

Andrew McPherson (andrew.mcpherson@gmail.com)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 nFuse

:: MORE INFORMATION

Citation:

McPherson AW, Wu C, Wyatt A, Shah SP, Collins C, Sahinalp SC.
nFuse: Discovery of complex genomic rearrangements in cancer using high-throughput sequencing.
Genome Res. 2012 Jun 28.

SUGEN v8.1 – Genetic Association Analysis Under Complex Survey Sampling

SUGEN v8.1

:: DESCRIPTION

SUGEN is a command-line software program written in C++ to implement the weighted and unweighted approaches for various types of association analysis under complex survey sampling.

::DEVELOPER

Danyu Lin

:: SCREENSHOTS

N/A

::REQUIREMENTS

  • Linux

:: DOWNLOAD

SUGEN

:: MORE INFORMATION

Citation

Lin DY, Tao R, Kalsbeek WD, Zeng D, Gonzalez F 2nd, Fernández-Rhodes L, Graff M, Koch GG, North KE, Heiss G.
Genetic association analysis under complex survey sampling: the Hispanic Community Health Study/Study of Latinos.
Am J Hum Genet. 2014 Dec 4;95(6):675-88. doi: 10.1016/j.ajhg.2014.11.005. PMID: 25480034; PMCID: PMC4259979.

SymmDock Beta 1.0 – Prediction of Complexes with Cn Symmetry

SymmDock Beta 1.0

:: DESCRIPTION

SymmDock is an algorithm for prediction of complexes with Cn symmetry by geometry based docking. Given the structure of the asymmetric unit of the multimer complex, SymmDock predicts the structure of the entire complex. A Cn symmetry type complex is a complex with a rotational symmetry of order n about a symmetry axis. The rotation angle alpha is of 360/n degrees.

::DEVELOPER

 the BioInfo3D group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

  SymmDock

:: MORE INFORMATION

Citation:

Schneidman-Duhovny D, Inbar Y, Nussinov R, Wolfson HJ.
PatchDock and SymmDock: servers for rigid and symmetric docking.
Nucl. Acids. Res. 33: W363-367, 2005

MultiWaver 2.0 – Modeling Discrete and Continuous Gene Flow to reconstruct Complex Population Admixtures

MultiWaver 2.0

:: DESCRIPTION

MultiWaver series software was designed to infer population admixture history in case of various and complex scenarios.

::DEVELOPER

Population Genomics Group (PGG)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

MultiWaver

:: MORE INFORMATION

Citation

Ni X, Yuan K, Liu C, Feng Q, Tian L, Ma Z, Xu S.
MultiWaver 2.0: modeling discrete and continuous gene flow to reconstruct complex population admixtures.
Eur J Hum Genet. 2019 Jan;27(1):133-139. doi: 10.1038/s41431-018-0259-3. Epub 2018 Sep 11. PMID: 30206356; PMCID: PMC6303267.

Whiteboard – C++ Framework for Programmatic Visualization of complex Biological Analysis

Whiteboard

:: DESCRIPTION

Whiteboard is a class library implemented in C++, allowing for easy graphing any kind of data into any format. Whiteboard provides all basic tool sets for drawing simple objects, as well as color manipulation methods, a rich set of compound graphs, and documentation.

::DEVELOPER

Grabherr Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOsX
  • C++ Compiler

:: DOWNLOAD

 Whiteboard 

:: MORE INFORMATION

Citation

Whiteboard: A framework for the programmatic visualization of complex biological analyses.
Sundström G, Zamani N, Grabherr MG, Mauceli E.
Bioinformatics. 2015 Feb 5. pii: btv078

DACO 1.03 – Transcription Factor Complex Prediction Algorithm

DACO 1.03

:: DESCRIPTION

DACO (domain-aware cohesiveness optimization) is a novel algorithm that combines protein-protein interaction networks and domain-domain interaction networks with the cluster-quality metric cohesiveness.

::DEVELOPER

Chair of Computational Biology at the Saarland University

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows/ MacOsX
  • Python

:: DOWNLOAD

 DACO

:: MORE INFORMATION

Citation

Bioinformatics. 2014 Sep 1;30(17):i415-i421. doi: 10.1093/bioinformatics/btu448.
Identifying transcription factor complexes and their roles.
Will T, Helms V.

Hyperscape – Visualization for Complex Biological Network

Hyperscape

:: DESCRIPTION

Hyperscape is a web server of visualization for complex biological networks.

::DEVELOPER

Parkinson lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Hyperscape: Visualization for complex biological networks.
Cromar GL, Zhao A, Yang A, Parkinson J.
Bioinformatics. 2015 Jun 24. pii: btv385.

TSSV 1.1.0 – Characterization of Complex Allelic Variants in pure and mixed Genomes

TSSV 1.1.0

:: DESCRIPTION

TSSV (Targeted characterisation of Short Structural Variation) is a program that does targeted characterisation of short structural variation. It can be used for STR analysis, or any other type of targeted analysis. It characterises any variation between a set of user-defined markers.

::DEVELOPER

TSSV team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows / MacOsX
  • Python

:: DOWNLOAD

  TSSV

:: MORE INFORMATION

Citation

TSSV: a tool for characterization of complex allelic variants in pure and mixed genomes.
Anvar SY, van der Gaag KJ, van der Heijden JW, Veltrop MH, Vossen RH, de Leeuw RH, Breukel C, Buermans HP, Verbeek JS, de Knijff P, den Dunnen JT, Laros JF.
Bioinformatics. 2014 Jun 15;30(12):1651-9. doi: 10.1093/bioinformatics/btu068

MM-align 20130815 – Protein Complex Structural Alignment

MM-align 20130815

:: DESCRIPTION

MM-align is an algorithm for structurally aligning multiple-chain protein-protein complexes. The algorithm is built on a heuristic iteration of a modified Needleman-Wunsch dynamic programming (DP) algorithm, with the alignment score specified by the inter-complex residue distances. The multiple chains in each complex are first joined, in every possible order, and then simultaneously aligned with cross-chain alignments prevented. The alignments of interface residues are enhanced by an interface-specific weighting factor.

::DEVELOPER

Yang Zhang’s Research Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
:: DOWNLOAD

 MM-align

:: MORE INFORMATION

Citation

S. Mukherjee, Y. Zhang,
MM-align: a quick algorithm for aligning multiple-chain protein complex structures using iterative dynamic programming.
Nucleic Acids Research 2009; 37: e83

simtrait – Simulate Complex Traits from Genotypes

simtrait

:: DESCRIPTION

The simtrait R package enables simulation of complex traits with user-set number of causal loci and the desired heritability of the trait (the proportion of variance due to genetic effects).

::DEVELOPER

The Ochoa Lab 

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ MacOsX / Windows
  • R

:: DOWNLOAD

simtrait

:: MORE INFORMATION