southern_blot_design 20090825 – Automated Design of Genomic Southern Blot Probes

southern_blot_design 20090825

:: DESCRIPTION

southern_blot_design is a novel software pipeline for designing and optimizing Southern blot probes in silico for use against genomic DNA targets.

::DEVELOPER

Genes to Cognition (G2C)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows/ MacOsX
  • Perl

:: DOWNLOAD

 southern_blot_design

:: MORE INFORMATION

Citation

BMC Genomics. 2010 Jan 29;11:74. doi: 10.1186/1471-2164-11-74.
Automated design of genomic Southern blot probes.
Croning MD1, Fricker DG, Komiyama NH, Grant SG.

SVDetect 0.8b – Detect Genomic Structural Variations from Paired-end and Mate-pair Sequencing data

SVDetect 0.8b

:: DESCRIPTION

SVDetect is a application for the isolation and the type prediction of intra- and inter-chromosomal rearrangements from paired-end/mate-pair sequencing data provided by the high-throughput sequencing technologies.

::DEVELOPER

Boeva lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 SVDetect

:: MORE INFORMATION

Citation:

Bioinformatics. 2010 Aug 1;26(15):1895-6.
SVDetect: a tool to identify genomic structural variations from paired-end and mate-pair sequencing data.
Zeitouni B, Boeva V, Janoueix-Lerosey I, Loeillet S, Legoix-né P, Nicolas A, Delattre O, Barillot E.

KGGSeq 1.2 – Genomic and Genetic studies using Sequence data

KGGSeq 1.2

:: DESCRIPTION

KGGSeq (Genomic and Genetic studies using Sequence data) is a software platform constituted of Bioinformatics and statistical genetics functions making use of valuable biologic resources and knowledge for sequencing-based genetic mapping of variants/genes responsible for human diseases/traits. Simply, KGGSeq is like a fishing rod facilitating geneticists to fish the genetic determinants of human diseases/traits in the big sea of DNA sequences. Compared with other genetic tools like plink/seq, KGGSeq paid more attention downstream analysis of genetic mapping. Currently, a comprehensive and efficient framework was newly implemented on KGGSeq to filter and prioritize genetic variants from whole exome sequencing data.

::DEVELOPER

Precision Medicine Genomics Laboratory

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux / MacOSX
  • Java

:: DOWNLOAD

 KGGSeq

:: MORE INFORMATION

Citation

Hum Mutat. 2015 Feb 10. doi: 10.1002/humu.22766.
wKGGSeq: A Comprehensive Strategy-Based and Disease-Targeted Online Framework to Facilitate Exome Sequencing Studies of Inherited Disorders.
Li MJ1, Deng J, Wang P, Yang W, Ho SL, Sham PC, Wang J, Li M.

Li MX, Gui HS, Kwan JS, Bao SY, Sham PC.
A comprehensive framework for prioritizing variants in exome sequencing studies of Mendelian diseases.
Nucleic Acids Res. 2012 Jan 12

RegTools 0.5.2 – Integrated analysis of Genomic and Transcriptomic data for discovery of Splicing Variants in Cancer

RegTools 0.5.2

:: DESCRIPTION

RegTools is a set of tools that integrate DNA-seq and RNA-seq data to help interpret mutations in a regulatory and splicing context.

::DEVELOPER

The Griffith Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/MacOsX
  • Python

:: DOWNLOAD

RegTools

:: MORE INFORMATION

Citation

RegTools: Integrated analysis of genomic and transcriptomic data for discovery of splicing variants in cancer
Yang-Yang Feng, et al.
doi: https://doi.org/10.1101/436634

KGGSEE 1.0 – Biological Knowledge-based Mining Platform for Genomic and Genetic association Summary statistics using gEne Expression

KGGSEE 1.0

:: DESCRIPTION

KGGSEE is a standalone Java tool for knowledge-based secondary analyses of genomic and genetic association summary statistics of complex phenotypes by integrating gene expression and related data. It has four major integrative analyses, 1) unconditional gene-based association guided by expression quantitative trait loci (eQTLs), 2) conditional gene-based association guided by selective expression in tissues or cell types, 3) estimation of phenotype-associated tissues or cell-type based on gene expression in single-cell or bulk cells of different tissues, and 4) causal gene inference for complex diseases and/or traits based-on multiple eQTL.

::DEVELOPER

Precision Medicine Genomics Laboratory

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux / MacOSX
  • Java

:: DOWNLOAD

KGGSEE

:: MORE INFORMATION

Citation

1. Xue C., et al. A global overview of single-cell type selectivity and pleiotropy in complex diseases and traits. In Submission (For estimation of phenotype-associated tissues or cell-type based on gene expression in single-cell or bulk cells of different tissues)

2. Jiang L., et al. Systematic comparative analysis of Mendelian randomization methods for inferring causal genes of complex phenotypes and the application to psychiatric diseases. In Submission (For causal gene inference for complex diseases and/or traits based-on multiple eQTL)

3. Li X.Y., et al. Gene-based association guided by eQTL. In Submission (For unconditional and condition gene-based association guided by eQTL)

GenePattern 3.9.11 – Genomic Analysis Platform

GenePattern 3.9.11

:: DESCRIPTION

GenePattern is a powerful genomic analysis platform that provides access to more than 125 tools for gene expression analysis, proteomics, SNP analysis and common data processing tasks. A web-based interface provides easy access to these tools and allows the creation of multi-step analysis pipelines that enable reproducible in silico research.

GenePattern provides access to a broad array of computational methods used to analyze genomic data. Its extendable architecture makes it easy for computational biologists to add analysis and visualization modules, which ensures that GenePattern users have access to new computational methods on a regular basis.

::DEVELOPER

The GenePattern team

:: SCREENSHOTS

:: REQUIREMENTS

  • Java VM
  • MacOSX/Windows/Linux
  • Other Java-enabled Platforms

:: DOWNLOAD

GenePattern

:: MORE INFORMATION

Citation

ATARiS: computational quantification of gene suppression phenotypes from multisample RNAi screens.
Shao DD, Tsherniak A, Gopal S, Weir BA, Tamayo P, Stransky N, Schumacher SE, Zack TI, Beroukhim R, Garraway LA, Margolin AA, Root DE, Hahn WC, Mesirov JP.
Genome Res. 2013 Apr;23(4):665-78. doi: 10.1101/gr.143586.112.

Reich M, Liefeld T, Gould J, Lerner J, Tamayo P, Mesirov JP
GenePattern 2.0
Nature Genetics 38 no. 5 (2006): pp500-501

GEMINI – The Genomic Search Engine

GEMINI

:: DESCRIPTION

GEMINI is an open-source bioinformatics tool and website written in python to facilitate near-neighbor searching of genomic data.

::DEVELOPER

Flaherty Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Python

:: DOWNLOAD

GEMINI

:: MORE INFORMATION

Citation

BMC Bioinformatics. 2016 Feb 24;17:102. doi: 10.1186/s12859-016-0934-8.
GEMINI: a computationally-efficient search engine for large gene expression datasets.
DeFreitas T, Saddiki H, Flaherty P

Magma 1.0 – Multiple Aligner of Genomic Multiple Alignments

Magma 1.0

:: DESCRIPTION

Magma is a fast, sensitive tool for whole regulome motif-finding in eukaryotic genomes

::DEVELOPER

Stormo Lab in Department of Genetics, Washington University

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • C++ Compiler
  • Perl

:: DOWNLOAD

 Magma

:: MORE INFORMATION

Citation

J Comput Biol. 2012 Feb;19(2):139-47. doi: 10.1089/cmb.2011.0249.
Fast, sensitive discovery of conserved genome-wide motifs.
Ihuegbu NE, Stormo GD, Buhler J.

MochiView 1.46 – Genomic Sequences Browser

MochiView 1.46

:: DESCRIPTION

MochiView is Java software that integrates browsing of genomic sequences, features, and data with DNA motif visualization and analysis

::DEVELOPER

the Johnson Lab

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / MacOsX /  Linux
  • Java

:: DOWNLOAD

 MochiView

:: MORE INFORMATION

Citation

Oliver R Homann and Alexander D Johnson
MochiView: versatile software for genome browsing and DNA motif analysis
BMC Biology 2010, 8:49