Tag: Genome-wide

Nucleosee – Visual Genome-wide search of Nucleosome Patterns

Nucleosee

:: DESCRIPTION

Nucleosome is web-based nucleosome map visual browser backed up by BWT-based pattern searches. It can be used for other kinds of high-throughput genomic data as well.

::DEVELOPER

The VisUsal (Visual Analytics and Information Visualization, Universidad de Salamanca) group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

Nucleosee

:: MORE INFORMATION

Citation

Santamaría, R., Therón, R., Durán, L., García, A., González, S., Sánchez, M., & Antequera, F. (2019).
Genome-wide search of nucleosome patterns using visual analytics.
Bioinformatics, 35(13), 2185-2192

KimTree 2.0.1 – Inferring Population Histories using Genome-wide Allele Frequency data

KimTree 2.0.1

:: DESCRIPTION

KimTree is a program aimed at estimating divergence times on a diffusion time scale from large single nucleotide polymorphism (SNP) data

::DEVELOPER

KimTree team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 KimTree

:: MORE INFORMATION

Citation

Gautier M and Vitalis R (2013)
Inferring population histories using genome-wide allele frequency data.
Molecular Biology and Evolution 30: 654-668

GEMMA 0.94.1 – Genome-wide Efficient Mixed Model Association

GEMMA 0.94.1

:: DESCRIPTION

GEMMA (Genome-wide Efficient Mixed Model Association) tests for association in genome-wide association studies (GWAS) using a standard linear mixed model to account for population stratification and sample structure. It calculates exact Wald or likelihood ratio test statistics and p-values, and is computationally efficient for large GWAS.

::DEVELOPER

Xiang Zhou

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 GEMMA

:: MORE INFORMATION

Citation

Nat Genet. 2012 Jun 17;44(7):821-4. doi: 10.1038/ng.2310.
Genome-wide efficient mixed-model analysis for association studies.
Zhou X, Stephens M.

ChIPDiff – Genome-wide Comparison of Histone Modification Sites Identified by ChIP-seq

ChIPDiff

:: DESCRIPTION

ChIPDiff provides a solution for the identification of Differential Histone Modification Sites (DHMSs) by comparing two ChIP-seq libraries (L1 and L2). An HMM is employed in ChIPDiff to infer the states of histone modification changes

:: DEVELOPER

Computational & Mathematical Biology Lab @ GIS

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • C Compiler

:: DOWNLOAD

 ChIPDiff

:: MORE INFORMATION

Citation

An HMM approach to genome-wide identification of differential histone modification sites from ChIP-seq data.
Xu H, Wei CL, Lin F, Sung WK.
Bioinformatics. 2008 Oct 15;24(20):2344-9

seqMINER 1.3.3e – Genome Wide Mapping data Interpretation Platform for NGS(ChIPSeq)

seqMINER 1.3.3e

:: DESCRIPTION

seqMINER is an integrated user friendly platform that allows addressing central questions in the ChIP-seq analysis workflow. The design of seqMINER was made in order to make it as easy as possible for an investigator to reach high level of interpretation on his dataset to answer its biological question at best.

::DEVELOPER

seqMINER Team

:: SCREENSHOTS

seqMINER

:: REQUIREMENTS

  • Linux / Mac OsX / Windows
  • Java

:: DOWNLOAD

 seqMINER

:: MORE INFORMATION

Citation

Nucleic Acids Res. 2011 Mar;39(6):e35. doi: 10.1093/nar/gkq1287. Epub 2010 Dec 21.
seqMINER: an integrated ChIP-seq data interpretation platform.
Ye T, Krebs AR, Choukrallah MA, Keime C, Plewniak F, Davidson I, Tora L.

SMART TOOLS – Implementation of a de novo Genome-wide Computational approach for updating Brachypodium miRNAs

SMART TOOLS

:: DESCRIPTION

SMART TOOLS  (smallRNA Team) comprises the moduleas:

  • Identification of stress-related small RNAs and miRNAs in plants.
  • Software development for discovery of novel miRNA genes in plant genomes.
  • Cancer-related miRNAs and their target sites
  • Promoter-associated small RNAs and methylation gene profile in plants.
  • Computational tools for small RNA annotation and expression profiling.

::DEVELOPER

University of Plovidv, Dept. Plant Physiology and Molecular Biology,

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 SMART TOOLS

:: MORE INFORMATION

Citation

Baev V, Milev I, Naydenov M, Apostolova E, Minkov G, Minkov I, Yahubyan G.
“Implementation of a de novo genome-wide computational approach for updating Brachypodium miRNAs”
Genomics. 2011 Feb 28. [Epub ahead of print] PMID: 21371551

shellfish – Parallel PCA and data processing for Genome-wide SNP data

shellfish

:: DESCRIPTION

shellfish carries out a variety of tasks related to principal component analysis of genome-wide SNP data. Unlike other available software, PCA computations can be carried out in parallel (both on a computing cluster running the Sun Grid Engine, and also in the simple case of a machine with multiple processors). In addition to the PCA calculations, it automates the process of data subsetting and allele-matching, using plink and gtool for file format interconversion where necessary. The aim is that tasks that would otherwise require a complex series of shell commands and/or work in R, can be carried out with a single, straightforward, command.

::DEVELOPER

Dan Davison

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • MacOsX / Linux
  • Python

:: DOWNLOAD

 shellfish

:: MORE INFORMATION

PeakAnalyzer 1.4 – Genome-wide Annotation of Chromatin Binding and Modification Loci.

PeakAnalyzer 1.4

:: DESCRIPTION

PeakAnalyzer is a Java GUI application comprising two main utilities:1. PeakAnnotator – for annotating genomic loci ,2. PeaksSplitter – for subdividing broad peaks into individual binding sites

::DEVELOPER

Bertone Group

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux / Windows / MacOsX
  • Java

:: DOWNLOAD

 PeakAnalyzer

:: MORE INFORMATION

Citation:

BMC Bioinformatics. 2010 Aug 6;11:415.
PeakAnalyzer: genome-wide annotation of chromatin binding and modification loci.
Salmon-Divon M, Dvinge H, Tammoja K, Bertone P.

COE 0.0.5 – Genome-Wide Two-Locus Epistasis Test in Disease Association Study

COE 0.0.5

:: DESCRIPTION

COE is a software for efficient large scale gene-gene interaction analysis, which supports a wide range of tests.

::DEVELOPER

the UNC Computational Genetics Working Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux
  • C Compiler

:: DOWNLOAD

 COE 

:: MORE INFORMATION

Citation

Xiang Zhang, Feng Pan, Yuying Xie, Fei Zou, and Wei Wang.
COE: A General Approach for Efficient Genome-Wide Two-Locus Epistasis Test in Disease Association Study
Journal of Computational Biology. March 2010, 17(3): 401-415. doi:10.1089/cmb.2009.0155.

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