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Links to deliverables and publications from FP7 projects, as well as links to some specific result types such as dataset and software, are dynamically retrieved from OpenAIRE .
Deliverables
We have developed a bio-informatics environment for genes (EST) mapping that includes:
-A database storing lab protocols. EST data, bibliographic information, mapping results, bioinformatics analysis results.
-Submission mechanisms based on Excel files or Web forms.
-Automatic sequence comparison and update with alert to the submitter.
-Synteny data consistency checking.
-WWW navigation interfaces and a graphical user interface for displaying and comparing maps.
-Links toward many external sources of related data.
-The environment is based on the EyeDB object-oriented database management system, and has been developed in C++, Java and some Perl. Access can be restricted by login/password, IP and HTTP filtering.
-The environment consists in a database schema, Perl and C++ programs for data submission and importation, automatic sequence comparison to private and public databases, alerting submitters on new hits, automatic synteny checking, database browsing and report generation; Java programs for data visualisation; associated electronic short documentation.
The environment has been specified by an international consortium of animal genomic experts and implemented within a leading bioinformatics centre. It Would be very valuable to re-use it in other EST mapping projects.
GENETPIG programme (study of GENes controlling Economic Traits in PIG) With the help of Europe, researchers have developed a pig genetic map. The current maps built with genetic markers is a basis tool for understanding genetic organisation and variation at the molecular level. At the beginning of the GENETPIG programme (1998), the number of known genes was relatively low (only 160 genes localised). With this level of map resolution, it is often difficult to identify closely linked markers allowing selection for agricultural traits and even more difficult to isolate the causal genes. A comprehensive catalogue of mapped genes must be created to more easily select candidate genes.
The driving GENETPIG idea was to begin the catalogue of pig genes. Given the conservation of structure of chromosomes between pigs and humans it is also highly desirable to use the large amount of human information already localised in this species. Our idea was to establish a maximum number of connections between these sources of markers serving as anchors across the other mammalian species maps. With the participation of four European countries (Denmark, France, Germany, Italy), the GENETPIG programme was to localise about 600 pig new genes from ovary, liver, muscle, small intestine tissues and about 100 already know human genes on the pig map. We obtained this result using the conventional somatic hybrid panel and for the best part the pig radiated hybrid panel. Today this method is the most effective ways to fulfil the cytogenetic map.
Knowledge: porcine ESTs, physically mapped.
Current state of the art: the identification and mapping of ESTs is one of the currently most important research work done in order to get insight into the transcriptome and the genes functions and interactions and in order to effectively make use of knowledge obtained in other species than pig (comparative mapping). At the starting point there were only a about 4000 porcine ESTs available in the public databases. Nowadays there are about 50.000 porcine ESTs sequenced. The project largely contributed to the improvement of the type I marker map of the pig.
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