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

KGGSeq 1.1 / wKGGSeq 20150119 – Genomic and Genetic studies using Sequence data

KGGSeq 1.1 / wKGGSeq 20150119

:: 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.

wKGGSeq is a framework facilitating comprehensive downstream analysis of next-generation sequencing data to identify causal mutation of human diseases for basic research and clinic diagnosis.

::DEVELOPER

Miao-xin Li, JJWang Lab

:: 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

Woods – A Functional Classifier of Genomic and Metagenomic Sequences

Woods

:: DESCRIPTION

Woods tool using an integrated approach for fast and accurate functional annotation of proteins in both genomic and metagenomic datasets.

::DEVELOPER

MetaBioSys laboratory

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Perl

:: DOWNLOAD

 Woods

:: MORE INFORMATION

GenePattern 3.9.7 – Genomic Analysis Platform

GenePattern 3.9.7

:: 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 at the Broad Institute of MIT and Harvard.

:: 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

BISQUE 1.0 – a human Genomic, Proteomic, and Transcriptomic Conversion tool

BISQUE 1.0

:: DESCRIPTION

BISQUE (The Biological Sequence Exchange) is a bioinformatics tool enabling locus and variant-specific conversion among human gene, transcript, and protein identifiers from several popular databases.

::DEVELOPER

Yu Lab 

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Python

:: DOWNLOAD

  BISQUE

:: MORE INFORMATION

Citation

BISQUE: locus- and variant-specific conversion of genomic, transcriptomic, and proteomic database identifiers.
Meyer MJ, Geske P, Yu H.
Bioinformatics. 2016 Jan 23. pii: btw043.

Dintor – Functional Annotation of Genomic and Proteomic data

Dintor

:: DESCRIPTION

Dintor is a data integration framework that provides a set of over 30 tools to assist researchers in the exploration of genomics and proteomics datasets.

::DEVELOPER

the Center of Biomedicine (CBM) at EURAC research.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 Dintor

:: MORE INFORMATION

Citation

Dintor: functional annotation of genomic and proteomic data.
Weichenberger CX, Blankenburg H, Palermo A, D’Elia Y, K?nig E, Bernstein E, Domingues FS.
BMC Genomics. 2015 Dec 21;16(1):1081. doi: 10.1186/s12864-015-2279-5.

Splign 20140625 – Compute cDNA-to-Genomic / Spliced Sequence Alignment

Splign 20140625

:: DESCRIPTION

Splign is a utility for computing cDNA-to-Genomic, or spliced sequence alignments. At the heart of the program is a compartmentization algorithm which identifies possible gene duplications, and a refined alignment algorithm recognizing introns and splice signals.

Splign Online Version

::DEVELOPER

NCBI

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows / Mac OsX

:: DOWNLOAD

Splign

:: MORE INFORMATION

Citation

Y.Kapustin, A.Souvorov, T.Tatusova and D.Lipman.
Splign: algorithms for computing spliced alignments with identification of paralogs.
Biology Direct, May 2008.

LOLA 1.0.0 – Genomic Locus Overlap Enrichment Analysis

LOLA 1.0.0

:: DESCRIPTION

LOLA (Locus Overlap Analysis) is an R Bioconductor package for genomic locus overlap enrichment. LOLA lets you test your genomic ranges of interest against a database of other genomic range sets to identify enrichment of overlap, tying external annotation to your regions of interest.

::DEVELOPER

Nathan Sheffield

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOsX / Windows
  • R
  • BioConductor

:: DOWNLOAD

 LOLA

:: MORE INFORMATION

Citation

LOLA: Enrichment analysis for genomic region sets and regulatory elements in R and Bioconductor.
Sheffield NC, Bock C.
Bioinformatics. 2015 Oct 27. pii: btv612.