GCUA 1.2 – Evaluate Codon Usage in a set of Genes

GCUA 1.2

:: DESCRIPTION

GCUA (General Codon Usage Analysis) is designed to perform various tasks that are of use for evaluating codon usage in a set of genes.  You can get it to do some simple things like calculate the number of observations of a particular codon in a gene.  Or you can do the same thing for the combined dataset.  You can also look at amino acid usage frequencies (again for each gene or for the dataset as a whole).  The program also produces a distance matrix based on the similarity of codon usage in genes.

::DEVELOPER

McInerney lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux / MacOS

:: DOWNLOAD

GCUA

:: MORE INFORMATION

Citation:

McInerney, J.O. (1998).
GCUA (General Codon Usage Analysis).
Bioinformatics: 14 (4) 372-373.

simDEF – Definition-based Semantic Similarity Measure of GO Terms for Functional Similarity Analysis of Genes

simDEF

:: DESCRIPTION

simDEF is an efficient method for measuring semantic similarity of GO terms using their GO definitions.

::DEVELOPER

Beiko lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Perl

:: DOWNLOAD

  simDEF

:: MORE INFORMATION

Citation:

simDEF: Definition-based Semantic Similarity Measure of Gene Ontology Terms for Functional Similarity Analysis of Genes.
Pesaranghader A, Matwin S, Sokolova M, Beiko RG.
Bioinformatics. 2015 Dec 26. pii: btv755.

isONclust 0.0.4 – de novo Clustering of long Transcript Reads into Genes

isONclust 0.0.4

:: DESCRIPTION

isONclust is a tool for clustering either PacBio Iso-Seq reads, or Oxford Nanopore reads into clusters, where each cluster represents all reads that came from a gene.

::DEVELOPER

Medvedev Group

:: SCREENSHOTS

N/A

::REQUIREMENTS

  • Linux / MacOsX
  • Python

:: DOWNLOAD

isONclust

:: MORE INFORMATION

Citation

Kristoffer Sahlin, Paul Medvedev (2019)
De Novo Clustering of Long-Read Transcriptome Data Using a Greedy, Quality-Value Based Algorithm“,
RECOMB 2019

gespeR 0.99.5 – Gene Specific Phenotype Estimator

gespeR 0.99.5

:: DESCRIPTION

gespeR estimates gene-specific phenotypes from off-target confounded RNAi screens. Observed phenotype for a specfic siRNA is modeled as a linear combination of gene-specific phenotypes from the on- and all off-target genes.

::DEVELOPER

the Computational Biology Group (CBG)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux / MacOsX
  • R package

:: DOWNLOAD

 gespeR

:: MORE INFORMATION

Citation

Fabian Schmich, Ewa Szczurek, Saskia Kreibich, Sabrina Dilling, Daniel Andritschke, Alain Casanova, Shyan Huey Low, Simone Eicher, Simone Muntwiler, Mario Emmenlauer, Pauli Ramo, Raquel Conde-Alvarez, Christian von Mering, Wolf-Dietrich Hardt, Christoph Dehio and Niko Beerenwinkel.
gespeR: a statistical model for deconvoluting off-target-confounded RNA interference screens
Genome Biology, 2015.

MetQy – Query Metabolic Functions of Genes and Genomes

MetQy

:: DESCRIPTION

MetQy (metabolic query) is a R package to ease interfacing with the Kyoto Encyclopedia of Genes and Genomes (KEGG) database to query metabolic functions of genes and genomes.

::DEVELOPER

OSS-Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows/ MacOs
  • R

:: DOWNLOAD

MetQy

:: MORE INFORMATION

Citation

Bioinformatics. 2018 Dec 1;34(23):4134-4137. doi: 10.1093/bioinformatics/bty447.
MetQy-an R package to query metabolic functions of genes and genomes.
Martinez-Vernon AS, Farrell F, Soyer OS

BosFinder – pre-microRNA Gene prediction algorithm in Bos taurus

BosFinder

:: DESCRIPTION

BosFinder is a new algorithm which was developed to identify and annotate the whole genome’s derived pre-miRNAs.

::DEVELOPER

Laboratory of Systems Biology & Bioinformatics (LBB)

:: SCREENSHOTS

BosFinder

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

 BosFinder

:: MORE INFORMATION

Citation

Anim Genet. 2014 May 17. doi: 10.1111/age.12170. [Epub ahead of print]
BosFinder: a novell pre-microRNA gene prediction algorithm in Bos taurus.
Sadeghi B1, Ahmadi H, Azimzadeh-Jamalkandi S, Nassiri MR, Masoudi-Nejad A.

NEMO 1.5.2 – Analyzing Gene and Chromosome Territory Distributions from 3D-FISH Experiments

NEMO 1.5.2

:: DESCRIPTION

NEMO is a new Smart 3D-FISH (Three-dimensional fluorescence in situ hybridization) graphical user interface which provides all information in the same place so that results can be checked and validated efficiently.

::DEVELOPER

NEMO team

:: SCREENSHOTS

NEMO

:: REQUIREMENTS

  • Windows / Linux / MacOsX
  • Java
  • ImageJ

:: DOWNLOAD

 NEMO

:: MORE INFORMATION

Citation

Bioinformatics. 2010 Mar 1;26(5):696-7. doi: 10.1093/bioinformatics/btq013. Epub 2010 Jan 14.
NEMO: a tool for analyzing gene and chromosome territory distributions from 3D-FISH experiments.
Iannuccelli E1, Mompart F, Gellin J, Lahbib-Mansais Y, Yerle M, Boudier T.

PsyGeNET v2 / Psygenet2r 1.4.0 – Knowledge Platform on Psychiatric Disorders and their Genes

PsyGeNET v2 / Psygenet2r 1.4.0

:: DESCRIPTION

PsyGeNET (Psychiatric disorders Gene association NETwork) is a resource for the exploratory analysis of psychiatric diseases and their associated genes.

Psygenet2r is an R package for querying PsyGeNET and to perform comorbidity studies in psychiatric disorders

::DEVELOPER

The Integrative Biomedical Informatics group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/windows/MacOsX
  • R

:: DOWNLOAD

Psygenet2r

:: MORE INFORMATION

Citation

Gutiérrez-Sacristán A, Grosdidier S, Valverde O, Torrens M, Bravo À, Piñero J, Sanz F, Furlong LI.
PsyGeNET: a knowledge platform on psychiatric disorders and their genes.
Bioinformatics. 2015 Sep 15;31(18):3075-7. doi: 10.1093/bioinformatics/btv301.

mBISON – Find Enrichment of miRNA Targets on lists of Genes

mBISON

:: DESCRIPTION

mBISON (Analysis on miRNA binding site over-representation) finds over-represented miRNA targets in a gene list you provide.

::DEVELOPER

Computational Biology and Data Mining (CBDM) Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

BMC Res Notes. 2015 Apr 16;8:157. doi: 10.1186/s13104-015-1118-8.
mBISON: Finding miRNA target over-representation in gene lists from ChIP-sequencing data.
Gebhardt ML, Mer AS, Andrade-Navarro MA.

 

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