EADGENE Bioinformatics Tools
The Bioinformatics departments at EADGENE institutes are involved in the development of various bioinformatics tools, some of which are listed below, with direct links to the tools provided on the right side of this page.
**NEW** CORNA
http://bioinformatics.oxfordjournals.org/cgi/content/abstract/btp059
CORNA, an R package, takes lists of genes and statistically tests for over-representation of miRNA targets in that gene list, thus suggesting whether or not the list of genes is regulated by particular microRNAs.
A tutorial exists here: http://corna.sf.net.
AlVira
http://bioinfo.genopole-toulouse.prd.fr/Alvira
The Alvira tool is a general purpose multiple sequence alignment viewer with a special emphasis on the comparative analysis of viral genomes. This new tool has been devised specifically to address the problem of the simultaneous analysis of a large number of viral strains. The multiple alignment is embedded in a graph that can be explored at different levels of resolution. It was developed using EADGENE funding and also with the support of The Laboratory of Cellular Genetics of INRA and Genopole Toulouse Midi-Pyrénées.
Ark Database
http://www.thearkdb.org
The ArkDB database system at Roslin Institute aims to provide a comprehensive public repository for genome mapping data from farmed and other animal Species. In doing so, it aims to provide a route in to genomic and other sequence from the initial viewpoint of linkage mapping, RH mapping, physical mapping or - possibly more importantly - QTL mapping data.
ASG Pathways Analysis Software
http://www.asgbioinformatics.wur.nl
The ASG-bioinformatics pipeline is a software tool for the analysis of microarray experiments (pre- and post-analyses) which is available through the website of the Animal Sciences Group (ASG), Lelystad, The Netherlands. The software is an easy to use set of PERL script that uses freely available data from the internet. You can access the script at the ASG website: http://www.asgbioinformatics.wur.nl but please note that the software is password protected. The webmaster will give you a password upon request via e-mail using the link on the website. [Read More]
ICCARE - Interspecific Comparative Clustering and Annotation foR Est
http://bioinfo.genopole-toulouse.prd.fr/iccare
INRA has developed the Iccare web tool which uses all the EST and mRNA sequences of public databases for an organism of interest (query species) and compares them to all the transcripts of one reference organism (Homo sapiens or Arabidopsis thaliana). The results are displayed according to the location of the genes on the chromosomes of the reference organism. Gene structure information and sequence similarities are combined in a graphical representation in order to pinpoint the nature of the transcript query sequence. Iccare thus provides information about EST clustering and ortholog detection in the major farm animals. All the sequences are screened for vectors and masked for known repeats with RepeatMasker. The masked sequences are subsequently compared to all the transcript sequences of the reference organism with the blastn option of the BLAST program. The results are filtered according to the expected value. This value is normalized in order to fit a standardized e-value of a comparison with a database of 1 million residues. Only similarities, or more precisely, using the terminology of BLAST, Highest Scoring Pair (HSP) with an expected value less than 10-5 are kept for further consideration (the complete blast output is also available). Finally, Iccare compiles the BLAST results, the mapping information of the reference organism and formats these results for the web site application.
Maviant
http://snp.agrsci.dk/maviant
Maviant has been developed by the University of Aarhus. Maviant is a multi-purpose alignment viewing and annotation tool. It reads alignments from assembly files like ACE and generate a web based view using html, javascript and png files, which makes it independant from the data source. The output generated by Maviant is referred to as a view and is opened using a browser. The web based solution supports a cross-platform environment and is independant of operative systems.
NARCISSE
http://bioinfo.genopole-toulouse.prd.fr/narcisse
Narcisse has been developed by INRA to display the comparisons beteween complete genome sequences. This site is not confined to the comparison between orthologous genes of the different species but is intended to extend that comparison to non-coding orthologous sequences as well. INRA is also planning to integrate both the Narcisse and Iccare (see above) tools into a single one. Currently, only the alignment between the bovine, human and mouse genomes are implemented.
Patrocles
http://www.patrocles.org/Patrocles.htm
Patrocles is a database of polymorphic miRNA-target interactions, developed by the Unit of Animal Genomicsin the Faculty of Veterinary Medicine, University of Liège.