MirCheck – Identify Plant miRNA Genes

MirCheck

:: DESCRIPTION

MIRcheck is a perl script designed to identify RNA sequences with secondary structures similar to plant miRNAs. It compares a potential miRNA and precursor against a set of secondary structure constraints derived from known plant miRNA precursors. The potential miRNA and precursor “pass” MIRcheck if all requirements are met, and “fail” MIRcheck if one or more is not.

::DEVELOPER

Bartel Lab at Whitehead Institute for Biomedical Research

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux/ Windows/MacOsX
perl

:: DOWNLOAD

MirCheck

:: MORE INFORMATION

Citation

Mol Cell. 2004 Jun 18;14(6):787-99.
Computational identification of plant microRNAs and their targets, including a stress-induced miRNA.
Jones-Rhoades MW, Bartel DP.

Knet – Finds Pairs of Genes with Similar Behavior across a Gene Expression dataset

Knet

:: DESCRIPTION

Knet finds pairs of genes with similar behavior across a gene expression dataset. It is intended to be used as a comparative tool to compare the network size (number of output rows) between N datasets with the same numbers of biological samples (input columns) and measured genes (input rows).

::DEVELOPER

Krawetz Lab

:: SCREENSHOTS

:: REQUIREMENTS

Windows/ Linux /MacOsX

:: DOWNLOAD

Knet

:: MORE INFORMATION

Citation

Platts, A.E., Lalancette, C., Emery, B.R., Carrell, D.T. and Krawetz, S.A. (2010)
Disease Progression And Solid Tumor Survival: A Transcriptome Decoherence Model.
Molecular and Cellular Probes. 24:53-60.

GSA-SNP 20130719 – Process SNP data as well as Gene and Haplotype data

GSA-SNP 20130719

:: DESCRIPTION

GSA-SNP is a gene set analysis software that can process SNP data as well as gene and haplotype data.

::DEVELOPER

Dr. Dougu Nam , Dr. Sangsoo Kim

:: SCREENSHOTS

:: REQUIREMENTS

Linux / Windows/ MacOsX
Java

:: DOWNLOAD

GSA-SNP

:: MORE INFORMATION

Citation

GSA-SNP: a general approach for gene set analysis of polymorphisms.
Nam D, Kim J, Kim SY, Kim S.
Nucleic Acids Res. 2010 Jul;38(Web Server issue):W749-54. doi: 10.1093/nar/gkq428. Epub 2010 May 25.

KaPPA-Average 1.0 – Convert Probe ID-based Gene Expression data to Gene ID-based Data

KaPPA-Average 1.0

:: DESCRIPTION

KaPPA-Average organizes such a multiple to multiple relationships between probe IDs and gene IDs, and processes probe ID-based gene expression data to convert to gene ID-based data. When a gene is detectable by several probes, the expression value of the gene is calculated as the average of the probe values.

::DEVELOPER

Kazusa DNA Research Institute

:: SCREENSHOTS

:: REQUIREMENTS

Linux / Windows / MacOsX
Java

:: DOWNLOAD

KaPPA-Average

:: MORE INFORMATION

DNA – Puzzle Game of Gene

DNA

:: DESCRIPTION

DNA offers a completely new spin on the action puzzle genre…one that’s unlike anything you’ve ever played before! Help biologist Dr. Rose Thompson with her experiments in the creation of new species of flowers! Combine different combinations of proteins and cells to cause chain reactions, which will help grow all kinds of amazing flowers. Play Action, Puzzle or Eternal game modes for a variety of excitement and challenges!

::DEVELOPER

Merscom

:: SCREENSHOTS

:: REQUIREMENTS

Windows

:: DOWNLOAD

DNA

:: MORE INFORMATION

Biomorphs 3.5 – Demonstrate Limitations of Selection Acting on Genes

Biomorphs 3.5

:: DESCRIPTION

Biomorphs is a program to demonstrate the potential and the limitations of selection acting on genes and development. The program uses a recursive procedure to “develop” a numerical genotype into an image made of branching and overlapping lines.Biomorphs shows the user a “biomorph” image together with a set of its offspring, differing from the parent by one or a few mutations, and chooses a favorite to become the parent of the next generation. Applying artificial selection, the user can evolve interesting– and surprisingly lifelike– “biomorphs.”

::DEVELOPER

The Queller/Strassmann Research Group at Washington University in St. Louis

:: SCREENSHOTS

:: REQUIREMENTS

Windows / Mac

:: DOWNLOAD

Biomorphs

:: MORE INFORMATION

DNA Slider – Tests Heterogeneity in the Polymorphism-to-divergence Ratio among Different Regions of a Gene

DNA Slider

:: DESCRIPTION

DNA Slider is program for performing four significance tests of heterogeneity in the ratio of polymorphic sites to fixed differences in DNA sequence data.

::DEVELOPER

John H. McDonald

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Windows/Linux/MacOsX

:: DOWNLOAD

DNA Slider

:: MORE INFORMATION

Citation

McDonald, J.H. 1998.
Improved tests for heterogeneity across a region of DNA sequence in the ratio of polymorphism to divergence.
Molecular Biology and Evolution 15: 377-384.

OrientationChecker 1.0 – Check Orientation of 16S rRNA Gene Sequences

OrientationChecker 1.0

:: DESCRIPTION

OrientationChecker is a simple tool for quickly locating the position of partial sequences within the 16S rRNA gene, and determining (and, if necessary, altering) their orientation, without the need for time-consuming multiple sequence alignments.

::DEVELOPER

Dr Kevin Ashelford

:: SCREENSHOTS

:: REQUIREMENTS

Windows / Linux / Mac OsX
Java

:: DOWNLOAD

OrientationChecker

:: MORE INFORMATION

Citation

KE Ashelford et al. (2006)
New Screening software shows that most recent large 16S rRNA gene clone libraries contain chimeras.
Applied and Environmental Microbiology, 72(9): 5734-5741.

GNAT 1.22 – Gene / Protein Named Entity Recognition and Normalization software

GNAT 1.22

:: DESCRIPTION

GNAT (Gene Name Normalization) is a library and web service capable of performing gene entity NER and normalization of biomedical articles. Mentions of genes and proteins in the articles are linked to to Entrez Gene identifiers.

::DEVELOPER

the Bergman lab.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux / Windows / MacOsX
Java

:: DOWNLOAD

GNAT

:: MORE INFORMATION

Citation

Hakenberg et al. (2011)
The GNAT library for local and remote gene mention normalization
Bioinformatics (2011) 27 (19): 2769-2771.

pubmed2ensembl – Link Publications in PubMed to Genes in Ensembl

pubmed2ensembl

:: DESCRIPTION

pubmed2ensembl is an extension to the BioMart system that links over 2,000,000 articles in PubMed to nearly 150,000 genes in Ensembl from 50 species.

::DEVELOPER

the Nenadic group & the Bergman lab.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux / Windows / MacOsX
Perl
Java
BioMart

:: DOWNLOAD

pubmed2ensembl

:: MORE INFORMATION

Citation

PLoS One. 2011;6(9):e24716. Epub 2011 Sep 29.
pubmed2ensembl: a resource for mining the biological literature on genes.
Baran J, Gerner M, Haeussler M, Nenadic G, Bergman CM.