software

software  DGD accepted for publication in PLOS ONE

The paper describing the construction and the content of this database had been accepted for publication and the article is now available on the PLOS ONE website. We improved the first release by adding data from GEO and GO database. These addition permitted to analyse the gene coexpression level and the annotation similarity inside each group of duplicated genes (see below).

 

The database is available here : http://dgd.genouest.org. A contact form is available on the official AnnotQTL website, you can leave a comment or ask for new species.

software  DGD website released!

The Duplicated Gene Database website has been released! This database provides a simple way to quickly and easily select groups of tandem duplicate or large groups of multigene family by gene identifier, chromosomal location and/or keywords. This database could be useful for various fields of applications (structural genomic, gene expression profiling, gene mapping, gene annotation) and could be expanded to others genomes as genomic annotations and peptide sequences are available.

homepage

http://dgd.genouest.org

software  AnnotQTL accepted for publication in the NAR 2011 webserver edition

NAR just have let us know that our manuscript of AnnotQTL has been accepted for publication. The manuscript will be online in 2-3 weeks! In addition to the first release of AnnotQTL, we have added several ‘missing’ features:

  • The assembly version and the date of the request are now inserted into the exported text file (TSV or XML).
  • You can now run multiple analyses of several QTL regions (via a specific form in the ‘submit a request’ section). Of course, in this ‘multiple analyses’ mode, the highlight features still work (but for a unique biological function, i.e.: reproduction trait for all the QTL regions).

AnnotQTL can be found at http://annotqtl.genouest.org. We have also decided to add new features in a close future (based on the referee’s comments), such as to define a genomic region based on the STS markers surrounding a QTL region. A contact form is available on the official AnnotQTL website, you can leave a comment or ask for new species. The article is available here.

software  AnnotQTL website has been released!

Recently, we have released a new website: AnnotQTL, a web tool designed to gather the functional annotation of different prominent website though limiting the redundancy of information.

The last steps of genetic mapping research programs require to closely analyze several QTL regions to select candidate genes for further studies. Despite the existence of several websites (NCBI genome browser, Ensembl Browser and UCSC Genome browser) or web tools (Biomart, Galaxy) to achieve this task, the selection of candidate genes is still laborious. Indeed, information available on the prominent websites slightly differs in terms of gene prediction and functional annotation, and some other websites provide extra-information that researchers may want to use. Merging and comparing this information can be done manually for one QTL containing few genes but would be hardly possible for many different QTL regions and dozen of genes. Here we propose a web tool that, for the region of interest, merges the list of genes available in NCBI and Ensembl, removes redundancy, adds the functional annotation of different prominent web site and highlights the genes for which the functional annotation fits the biological function or diseases of interest. This tool is dedicated to sequenced livestock animal species (cattle, pig, chicken, and horse) and the dog as they have been extensively studied (indeed, more than 8000 QTL were detected).

The AnnotQTL server could be found here : http://annotqtl.genouest.org/

software  G3C

What is G3C ?

We have developed a software package called G3C (for Get all Co-annotated Co-located Clusters) using the PERL language. This software has been designed to identify all groups of co-located genes, which share a similar GO annotation on a genome scale. Basically, the principle of the software is the following: within a genomic window, it computes a p-value of the existence of a cluster of co-annotated genes for a specific similarity group of GO terms given by the hypergeometric distribution.

How does it work?

You need a functional PERL environment to use the software (the needed modules are mentioned in the online documentation). You will also need a SQL database to store data (pre-processing scripts are in the package).

Source

To download the G3C package, click on the following link: coming soon

software  MarketSet

What is MarkerSet?

MarkerSet is a command-line tool designed for selection of marker panel(s) according to genomic location and known informativity on experimental crosses (e.g. for wide genome scan). MarkerSet can be used with either SNP or microsatellite markers, because it only relies on informativity data. Basically, the algorithm will select the most informative markers in two windows separated by a constant gap, and sliding on the genome. MarkerSet will define automatically the windows size and the gap distance between the two windows depending on the wished number of markers to select and genome size. MarkerSet has several options to optimize markers selection with the possibility to give more weight to the markers distances or to the markers informativity. In case of availability of several experimental designs, it is possible to compare the markers set quality obtained by selecting markers perfectly fitted for each experimental design (monodesign selection), or by selecting a set of markers common to all designs (multidesign selection).

MarkerSet is designed to be compatible with any kind of markers and species.

What do I need to run MarkerSet?

MarkerSet needs a functional PERL environment with POSIX module available (typically *nix system, may work with MacOS X). MarkerSet.pl and config.pm files must be installed in the same directory.

The input file must be a plain tabulated text file with the following informations (headers are requested):

Markers name – chromosome – genomic location – informativity values for cross 1 (typically the number of heterozygote founders) – informativity values for cross 2 …

The available download package comes with core files (PERL program and config file), README file for explanations on program parameters, example input files, and a verbose log file for a better understanding of the algorithm.

Source

To download the markerset package, click on the following link: markerset_package.tar.gz

The article about this software could be found at BMC research Notes and the INSTALL and USAGE documentation can be found here.