LSGSP – Large-Scale Genome Sequence Processing

LSGSP

:: DESCRIPTION

LSGSP is the java codes which provided for use on this site are not part of the book Large-Scale Genome Sequence Processing published by Imperial College Press

::DEVELOPER

Masahiro Kasahara & Shinichi Morishita

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Linux/MacOsX
  • Java

:: DOWNLOAD

 LSGSP

:: MORE INFORMATION

 

IGD – A high-performance Search Engine for large-scale Genomic Interval Datasets

IGD

:: DESCRIPTION

IGD (integrated genome database) is a method and tool for searching genome interval datasets more than three orders of magnitude faster than existing approaches, while using only one hundredth of the memory.

::DEVELOPER

Sheffield lab of computational biology

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Python

:: DOWNLOAD

IGD

:: MORE INFORMATION

Citation

Feng J, Sheffield NC.
IGD: high-performance search for large-scale genomic interval datasets.
Bioinformatics. 2020 Dec 26:btaa1062. doi: 10.1093/bioinformatics/btaa1062. Epub ahead of print. PMID: 33367484.

DupTree – Large Scale Gene Tree Parsimony Analysis

DupTree

:: DESCRIPTION

DupTree is a program for large-scale phylogenetic analyses using gene tree parsimony.The program implements a novel algorithm that significantly improves upon the run time of standard search heuristics for gene tree parsimony, and enables the first truly genome-scale phylogenetic analyses.

::DEVELOPER

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

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux / Mac OsX

:: DOWNLOAD

  DupTree

:: MORE INFORMATION

Citation

DupTree: A program for large-scale phylogenetic analyses using gene tree parsimony
Andre Wehe, Mukul S. Bansal, J. G. Burleigh, Oliver Eulenstein.
Bioinformatics, 24(13): 1540-1541, 2008.

InterViewer 4.0 – Visualize Large-scale Protein Interaction Networks

InterViewer 4.0

:: DESCRIPTION

InterViewer is a software for visualizing large-scale protein interaction networks. InterViewer  (1) first finds a layout of connected components of an entire network, (2) finds a global layout of nodes with respect to pivot nodes within a connected component, and (3) refines the local layout of each connected component by first relocating midnodes with respect to their cutvertices and direct neighbors of the cutvertices and then by relocating all nodes with respect to their neighbors within distance 2. Advantages of InterViewer over classical graph drawing methods include: (1) it is an order of magnitude faster, (2) it can directly visualize data from protein interaction databases, and (3) it provides several operations for effectively exploring large-scale protein interaction networks.

::DEVELOPER

Biocomputing Lab. School of Computer Science and Engineering Inha University, Inchon

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / MacOsX / Linux
  • Java

:: DOWNLOAD

InterViewer

:: MORE INFORMATION

Citation

Byong-Hyon Ju, Byungkyu Park, Jong H. Park and Kyungsook Han
Visualization and analysis of protein interactions
Bioinformatics (2003) 19 (2): 317-318.

phenomeImpute 1.0 – R package to Impute Missing values in large-scale High-dimensional Phenome data

phenomeImpute 1.0

:: DESCRIPTION

phenomeImpute is an R package to impute missing values in large-scale high-dimensional phenome data. It includes several variations of KNN, random forest and MICE methods.

::DEVELOPER

George C. Tseng 

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 phenomeImpute

:: MORE INFORMATION

Citation

Liao SG, Lin Y, Kang DD, Chandra D, Bon J, Kaminski N, Sciurba FC, Tseng GC.
Missing value imputation in high-dimensional phenomic data: imputable or not, and how?
BMC Bioinformatics. 2014 Nov 5;15(1):346. doi: 10.1186/s12859-014-0346-6. PMID: 25371041; PMCID: PMC4228077.

SNAVI 20081120 – Analysis and Visualization of Large-Scale Cell Signaling Networks

SNAVI 20081120

:: DESCRIPTION

SNAVI (Signaling Networks Analysis and Visualization) is a Windows-based desktop application that implements standard network analysis methods to compute the clustering, connectivity distribution, and detection of network motifs, as well as provides means to visualize networks and network motifs. SNAVI is capable of generating linked web pages from network datasets loaded in text format. SNAVI can also create networks from lists of gene or protein names. SNAVI is a useful tool for analyzing, visualizing and sharing cell signaling data. SNAVI is open source free software.

::DEVELOPER

Ma’ayan Laboratory

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

 SNAVI

:: MORE INFORMATION

Citation

BMC Syst Biol. 2009 Jan 20;3:10. doi: 10.1186/1752-0509-3-10.
SNAVI: Desktop application for analysis and visualization of large-scale signaling networks.
Ma’ayan A, Jenkins SL, Webb RL, Berger SI, Purushothaman SP, Abul-Husn NS, Posner JM, Flores T, Iyengar R.

HAC 1.2.1 – Hierarchical Agglomerative Clustering for a large-scale Network data

HAC 1.2.1

:: DESCRIPTION

HAC is developed for fast clustering of heterogeneous interaction networks.

::DEVELOPER

Joel Bader lab

:: SCREENSHOTS

N/A

::REQUIREMENTS

  • Linux

:: DOWNLOAD

 HAC

:: MORE INFORMATION

Citation

BMC Bioinformatics. 2011 Feb 15;12 Suppl 1:S44. doi: 10.1186/1471-2105-12-S1-S44.
Resolving the structure of interactomes with hierarchical agglomerative clustering.
Park Y, Bader JS.

MegaDot 0.9 – Large Scale Dot Plotter

MegaDot 0.9

:: DESCRIPTION

MegaDot is a large scale dot plotter which is capable of producing dot density plots of tens of megabases of DNA sequence on a modest sized desktop machine, and of entire mammalian chromosomes on server scale computers.

::DEVELOPER

Human Genome Sequencing Center, Baylor College of Medicine

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows  / Linux / MacOsX
  • Java

:: DOWNLOAD

 MegaDot

:: MORE INFORMATION

Giggle v0.6.3 – Search Engine for large-scale integrated Genome Analysis

Giggle v0.6.3

:: DESCRIPTION

Giggle is a genomics search engine for genomic features and intervals. That is, scalable, multi-file index for fast queries of genomic intervals.

::DEVELOPER

The Quinlan Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Python

:: DOWNLOAD

Giggle

:: MORE INFORMATION

Citation:

Nat Methods. 2018 Feb;15(2):123-126. doi: 10.1038/nmeth.4556. Epub 2018 Jan 8.
GIGGLE: a search engine for large-scale integrated genome analysis.
Layer RM, Pedersen BS, DiSera T, Marth GT, Gertz J, Quinlan AR

MUMmer 4.0.0Beta2 / pymummer 0.11.0 – Alignment of Large-scale DNA & Protein Sequences

MUMmer 4.0.0Beta2/ pymummer 0.11.0

:: DESCRIPTION

MUMmer is a system for rapidly aligning entire genomes, whether in complete or draft form.MUMmer can also align incomplete genomes; it can easily handle the 100s or 1000s of contigs from a shotgun sequencing project, and will align them to another set of contigs or a genome using the NUCmer program included with the system. If the species are too divergent for a DNA sequence alignment to detect similarity, then the PROmer program can generate alignments based upon the six-frame translations of both input sequences.

pymummer is Python3 module for running MUMmer and reading the output

::DEVELOPER

MUMmer team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • GCC / Python

:: DOWNLOAD

MUMmer, pymummer

:: MORE INFORMATION

MUMmer is now an open source project.

Citation:

MUMmer4: A fast and versatile genome alignment system
G. Marçais , A.L. Delcher, A.M. Phillippy, R. Coston, S.L. Salzberg, A. Zimin,
PLoS computational biology (2018), 14(1): e1005944.

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