CRML – Locating Muscle-specific Regulatory Modules in C. elegans Sequences

CRML

:: DESCRIPTION

CRML (C. elegans Muscle Cis-Regulatory Module Locator) is a web tool for predicting cis-regulatory modules that direct muscle-specific gene expression in C. elegans. CRML makes high quality predictions with a sensitivity of 88% and a positive predictive value of at least 65%. In vivo experimental tests of 12 predicted modules show that 10 of those drive muscle-specific gene expression. These results suggest that CRML is highly accurate in identifying functional sequences important for muscle-specific gene expression and is a valuable tool for guiding experimental designs.

::DEVELOPER

Stormo Lab in Department of Genetics, Washington University

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Guoyan Zhao, Lawrence A. Schriefer and Gary D. Stormo (2007)
Identification of Muscle-Specific Regulatory Modules in Caenorhabditis elegans.
Genome Research. 17:348-357

QuantWorm 20130919 – Quantitative Phenotyping of C. Elegans

QuantWorm 20130919

:: DESCRIPTION

QuantWorm is a software package for automatic phenotyping in C. elegans.

:: DEVELOPER

Zhong’s lab

:: SCREENSHOTS

QuantWorm

:: REQUIREMENTS

  • Linux / windows/ MacOsX
  • JRE

:: DOWNLOAD

 QuantWorm

:: MORE INFORMATION

Citation

QuantWorm: a comprehensive software package for Caenorhabditis elegans phenotypic assays.
Jung SK, Aleman-Meza B, Riepe C, Zhong W.
PLoS One. 2014 Jan 8;9(1):e84830. doi: 10.1371/journal.pone.0084830.

MosLocator – Identification of Mos1 Insertions in the C.elegans Genome

MosLocator

:: DESCRIPTION

MosLocator is a tool for researchers who wish to look for insertions in or near one or many genes. It sends queries to a local database; depending on the number of queries and connection speeds, it may take a few seconds or even a couple of minutes for the answer to come back.

::DEVELOPER

the Ewbank lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

PLoS One. 2012;7(2):e30482. doi: 10.1371/journal.pone.0030482. Epub 2012 Feb 8.
A genome-wide collection of Mos1 transposon insertion mutants for the C. elegans research community.
Vallin E1, Gallagher J, Granger L, Martin E, Belougne J, Maurizio J, Duverger Y, Scaglione S, Borrel C, Cortier E, Abouzid K, Carre-Pierrat M, Gieseler K, Ségalat L, Kuwabara PE, Ewbank JJ.

ICeE 2.10 – Interface for C. Elegans Experiments

ICeE 2.10

:: DESCRIPTION

ICeE is a database with a Web-browser interface that allows you to enter experiments for the nematode C. elegans and to search efficiently in this database.

::DEVELOPER

the Ewbank lab

:: SCREENSHOTS

ICeE

:: REQUIREMENTS

  • Windows/ Linux/ MacOsX
  • Apache httpd
  • MySQL
  • PHP

:: DOWNLOAD

 ICeE

:: MORE INFORMATION

CellExplorer 1.0 – 3D C. elegans atlas Building & Application Tools

CellExplorer 1.0

:: DESCRIPTION

CellExplorer is a package of computer programs to process and analyze 3D confocal image stacks of the model animal C. elegans, and can be applied to several other model systems such as fruit fly embryo/larvae as well. Some other applications include 3D cell/nuclei segmentation, quantification, gene expression analysis, automatic cell naming/annotation, cell targeting, etc.

::DEVELOPER

Peng Lab @ JANELIA of HHMI

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux / Mac OsX
  • MATLAB

:: DOWNLOAD

CellExplorer

:: MORE INFORMATION

Citation:

Fuhui Long, Hanchuan Peng, Xiao Liu, Stuart Kim, and Eugene Myers,
A 3D digital atlas of C. elegans and its application to single-cell analyses,”
Nature Methods, doi:10.1038/nmeth.1366, 2009.

NetGene2 2.42 – Intron Splice Sites in Human, C. Elegans & A. Thaliana DNA

NetGene2 2.42

:: DESCRIPTION

NetGene2 is a service producing neural network predictions of splice sites in human, C. elegans and A. thaliana DNA.

::DEVELOPER

CBS (Center for Biological Sequence Analysis),  Technical University of Denmark

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

NetGene2 Source Code

:: MORE INFORMATION

Citation

S.M. Hebsgaard, P.G. Korning, N. Tolstrup, J. Engelbrecht, P. Rouze, S. Brunak
Splice site prediction in Arabidopsis thaliana DNA by combining local and global sequence information
Nucleic Acids Research, 1996, Vol. 24, No. 17, 3439-3452.

Brunak, S., Engelbrecht, J., and Knudsen, S.
Prediction of Human mRNA Donor and Acceptor Sites from the DNA Sequence
Journal of Molecular Biology, 1991, 220, 49-65.