Tag: Gene

Event-mapper 2.53 – Find Temporal on/off Switches shared by many Genes

Event-mapper 2.53

:: DESCRIPTION

Event-mapper is a tool to map gene expression events, such as on/off switches on a space define by the event time and duration. Massive changes in gene expression will appear as peaks (or clusters) in the output. E-mapper Input is a time-series data set, treated with RZ-smooth. E-mapper also requires an input pattern (sample patterns are provided). To plot and explore Event-mapper data you need to process it with Glob-mapper.

::DEVELOPER

Dmitri Papatsenko

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

 Event-mapper

:: MORE INFORMATION

Citation

Goltsev Y, Papatsenko D.
“Time warping of evolutionary distant temporal gene expression data based on noise suppression”
BMC Bioinformatics. 2009 Oct 26;10:353.

 

COGRIM – Clustering of Genes into Regulons using Integrated Modeling

COGRIM

:: DESCRIPTION

COGRIM is an R program of Bayesian hierarchical model and Gibbs Sampling implementation that integrates gene expression, ChIP binding, and transcription factor motif data in a principled and robust fashion.

::DEVELOPER

the Computational Biology and Informatics Laboratory (in the Center for Bioinformatics at the University of Pennsylvania)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 COGRIM

:: MORE INFORMATION

Citation:

G. Chen, S. T. Jensen, C. Stoeckert,
“Clustering of Genes into Regulons using Integrated Modeling-COGRIM“,
Genome Biology, 2007, Jan. 4;8(1):R4

COCO-CL – Identify Orthologous set of Genes.

COCO-CL

:: DESCRIPTION

COCO-CL (COrrelation COefficient-based CLustering) is a software for hierarchical clustering of orthology/homology relations, and identificationof orthologous groups of genes.

::DEVELOPER

Raja Jothi

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows / MacOsX
  • perl 

:: DOWNLOAD

 COCO-CL

:: MORE INFORMATION

Citation

Raja Jothi, et al
COCO-CL: Hierarchical Clustering of Homology Relations Based on Evolutionary Correlations
Bioinformatics. 2006 April 1; 22(7): 779–788.

MAGprediction – Gene Allele Prediction Using Unphased SNP data

MAGprediction

:: DESCRIPTION

MAGprediction (Multi-allelic Gene Prediction) is a software which was developed for predicting highly polymorphic gene alleles using unphased SNP data.

::DEVELOPER

Fred Hutchinson Cancer Research Center

:: SCREENSHOTS

:: REQUIREMENTS

:: DOWNLOAD

 MAGprediction

:: MORE INFORMATION

Citation

Li SS, Wang H, Smith A, Zhang B, Zhang XC, Schoch G, Geraghty D, Hansen JA, Zhao LP
Predicting Highly Polymorphic Alleles Using Unphased and Flanking Single Nucleotide Polymorphisms.
Genetic Epidemiology 2011,35(2):85-92

Sub-GSE – Testing Gene Set Enrichment for Subset of Genes

Sub-GSE

:: DESCRIPTION

SubGSE is developed for gene set enrichment analysis.The primary objective of this program is to measure the enrichment of differentially expressed or phenotype associated genes in given gene sets. The input for the program includes the gene expression data of several samples with corresponding phenotypic data (categorical or continuous), and several given gene sets. The program will assess the significance of the enrichment of genes, whose gene expression profiles are associated with the phenotypic data, in each given gene set.

::DEVELOPER

Fengzhu Sun

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux

:: DOWNLOAD

  SubGSE

:: MORE INFORMATION

Citation

Xiting Yan and Fengzhu Sun
Testing gene set enrichment for subset of genes: Sub-GSE
BMC Bioinformatics 2008, 9:362

BioMyn – Mining Gene and Protein Knowledge

BioMyn

:: DESCRIPTION

BioMyn is a comprehensive online resource that integrates information related to human genes and proteins from over a dozen external databases. It includes Gene Ontology annotations of human genes and proteins, sequence family classifications, protein domain architectures, metabolic and signaling pathways, protein interactions and protein complexes, and disease associations.

::DEVELOPER

Max-Planck-Institut Informatik

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 BioMyn

:: MORE INFORMATION

ProbeLynx 1.2.2 – Update the Association of Microarray Probes to Genes

ProbeLynx 1.2.2

:: DESCRIPTION

ProbeLynx is a web-based tool for updating the association of microarray probes to genes. using the latest genomics sequence information and experimentally determined cross-hybridization cutoffs, ProbeLynx allows users to upload microarray probe sequences to re-examine probe specificity and provide annotation updates relevant to determining which gene(s) and transcript(s) are associated with a given probe.

::DEVELOPER

Brinkman Laboratory, Simon Fraser University

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 ProbeLynx

:: MORE INFORMATION

Citation

Roche FM, Hokamp K, Acab M, Babiuk LA, Hancock RE, Brinkman FS.
ProbeLynx: a tool for updating the association of microarray probes to genes.
Nucleic Acids Res. 2004 Jul 1;32(Web Server issue):W471-4. PMID: 15215432

GeneTree 1.3 – Compare Gene and Species Trees

GeneTree 1.3

:: DESCRIPTION

GeneTree is an experimental program for comparing gene and species trees. The program can compute the cost of embedding a gene tree within a species tree, visually display the location and number of gene duplications and losses, and search for optimal species trees.

::DEVELOPER

Professor Rod Page

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / PowerMac

:: DOWNLOAD

GeneTree for win , for Power Macintosh

:: MORE INFORMATION

Citation

R D Page
GeneTree: comparing gene and species phylogenies using reconciled trees.
Bioinformatics. 1998;14(9):819-20.

Orphelia – Predict Genes in Metagenomic Sequencing Reads

Orphelia

:: DESCRIPTION

Orphelia is a metagenomic ORF finding tool for the prediction of protein coding genes in short, environmental DNA sequences with unknown phylogenetic origin [1]. Orphelia is based on a two-stage machine learning approach that was recently introduced by our group. After the initial extraction of open reading frames (ORFs), linear discriminants are used to extract features from those ORFs. Subsequently, an artificial neural network combines the features and computes a gene probability for each ORF in a fragment. A greedy strategy computes a likely combination of high scoring ORFs with an overlap constraint.

Orphelia Online Version

::DEVELOPER

the Department of Bioinformatics of the University of Göttingen

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

Orphelia

:: MORE INFORMATION

Citation

K. J. Hoff, T. Lingner, P. Meinicke, M. Tech (2009)
Orphelia: predicting genes in metagenomic sequencing reads
Nucleic Acids Research, 37:W101-W105.

TOUR OF THE BASICS – Introduce DNA & Genes

TOUR OF THE BASICS

:: DESCRIPTION

TOUR OF THE BASICS is a flash animated tour of  DNA & Genes.

::DEVELOPER

Genetic Science Learning Center

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / Mac OsX

:: DOWNLOAD

TOUR OF THE BASICS for win ; for MacOsX

:: MORE INFORMATION

Funding provided by a grant from The R. Harold Burton Foundation.

 

Exit mobile version