GraPPLE – Graph Property based Predictor and Likelihood Estimator

GraPPLE

:: DESCRIPTION

GraPPLE are abstract representations of relationships between entities. Through a set of instructions, they are able to convert relationships into nodes and edges. GraPPLE (originally: The RNA sorting hat) leverages the information available from graph properties and the predictive power of support vector machines (SVMs) to classify potential RNA sequences as functional/non-functional and into 1 of 46 Rfam families. In short, GraPPLE predicts the potential function of an ncRNA sequence.

::DEVELOPER

Max Planck Institute for Molecular Plant Physiology

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Nucleic Acids Res. 2009 May;37(9):e66. Epub 2009 Apr 1.
Identification and classification of ncRNA molecules using graph properties.
Childs L, Nikoloski Z, May P, Walther D.

BCALM 2.2.1 – de Bruijn Graph Compacation from Reads

BCALM 2.2.1

:: DESCRIPTION

BCALM is a bioinformatics tool for constructing the compacted de Bruijn graph from sequencing data.

::DEVELOPER

Medvedev Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

BCALM

:: MORE INFORMATION

Citation:

Rayan Chikhi, Antoine Limasset and Paul Medvedev,
Compacting de Bruijn graphs from sequencing data quickly and in low memory,
Bioinformatics, 32 (12), i201-i208 2016 Jun 15

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

GRAPES 2.9 – SMP Querying system for Efficient Parallel Subgraph Isomorphism in databases of Graphs

GRAPES 2.9

:: DESCRIPTION

GRAPES is a querying system for parallel searching in databases of graphs, and single target graph, using symmetric multiprocessing (SMP) architectures. It implements a parallel version of well established graph searching algorithms providing efficient solutions for graphs indexing and matching.

::DEVELOPER

Alfredo Pulvirenti

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 GRAPES

:: MORE INFORMATION

Citation:

GRAPES: a software for parallel searching on biological graphs targeting multi-core architectures.
Giugno R, Bonnici V, Bombieri N, Pulvirenti A, Ferro A, Shasha D.
PLoS One. 2013 Oct 22;8(10):e76911. doi: 10.1371/journal.pone.0076911.

Recycler v0.7 – Detecting Plasmids from de novo Assembly Graphs

Recycler v0.7

:: DESCRIPTION

Recycler is a tool for extracting cyclical sequences from assembly graphs that are likely to be plasmids, phages, or other mobile elements that are physically separate from their host genomes. It can be applied on isolate, metagenome, and plasmidome graphs.

::DEVELOPER

Ron Shamir’s lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Python

:: DOWNLOAD

Recycler

:: MORE INFORMATION

Citation

Bioinformatics. 2017 Feb 15;33(4):475-482. doi: 10.1093/bioinformatics/btw651.
Recycler: an algorithm for detecting plasmids from de novo assembly graphs.
Rozov R, Brown Kav A, Bogumil D, Shterzer N, Halperin E, Mizrahi I, Shamir R.

Faucet v0.5 – Streaming de novo Assembly Graph Construction

Faucet v0.5

:: DESCRIPTION

Faucet is an streaming metagenome assembler. It uses low memory and disk space and achieves highly contiguous assemblies.

::DEVELOPER

Ron Shamir’s lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

Faucet

:: MORE INFORMATION

Citation

Bioinformatics. 2018 Jan 1;34(1):147-154. doi: 10.1093/bioinformatics/btx471.
Faucet: streaming de novo assembly graph construction.
Rozov R, Goldshlager G, Halperin E, Shamir R.

GRAPHITE – Graph-based Variant Adjudication

GRAPHITE

:: DESCRIPTION

Graphite is a variant adjudication tool that aids in confirming or rejecting the presence of candidate alleles by constructing a graph using reference as well as alternate alleles.

::DEVELOPER

The MarthLab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

Graphite

:: MORE INFORMATION

GraphDTL v004 – Graph Reconciliation for Species Tree S and Gene Tree G

GraphDTL v004

:: DESCRIPTION

GraphDTL is the first method to infer supports for evolutionary events based on their frequencies in the set of equally parsimonious reconciliations
Given a , this program computes

::DEVELOPER

The Computational Biology Institute (IBC)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 GraphDTL

:: MORE INFORMATION

Citation

J Bioinform Comput Biol. 2013 Apr;11(2):1250025. doi: 10.1142/S0219720012500254. Epub 2012 Dec 28.
Representing a set of reconciliations in a compact way.
Scornavacca C1, Paprotny W, Berry V, Ranwez V.

SeqGrapheR 0.4.8.5 – Graph based Visualization of Cluster of DNA sequence reads

SeqGrapheR 0.4.8.5

:: DESCRIPTION

 SeqGrapheR package provide interactive GUI for visualization of DNA sequence clusters.

::DEVELOPER

Laboratory of Molecular CytogeneticsInstitute of Plant Molecular Biology ,Biology Centre ASCR

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux / Windows / MacOsX
  • R package

:: DOWNLOAD

 SeqGrapheR

:: MORE INFORMATION

Citation

Graph-based clustering and characterization of repetitive sequences in next-generation sequencing data
Petr Novák, Pavel Neumann and Jiří Macas
BMC Bioinformatics 2010, 11:378

Bandage v0.7.1 – Navigating De novo Assembly Graphs Easily

Bandage v0.7.1

:: DESCRIPTION

Bandage (a B: ioinformatics A: pplication for N: avigating De novo A: ssembly G: raphs E: asily)  is a GUI program that allows users to interact with the assembly graphs made by de novo assemblers Velvet and SPAdes.

::DEVELOPER

Ryan Wick rrwick@gmail.com

:: SCREENSHOTS

Bandage

:: REQUIREMENTS

  • Windows/ Linux/ MacOsX

:: DOWNLOAD

 Bandage

:: MORE INFORMATION

Citation:

Bandage: interactive visualisation of de novo genome assemblies.
Wick RR, Schultz MB, Zobel J, Holt KE.
Bioinformatics. 2015 Jun 22. pii: btv383