Clustering d'EST

Virginie Garcia, Aurélien Barré

Maritime pine (Pinus pinaster Ait.) has reached genomic investigation at the "laboratoire de génétique et amélioration des arbres forestiers" of INRA (Pierroton), within the "LIGNOME" program. This program aims at studying the genome and proteome of lignous species, with a focus on environmental adaptation and quality production. In Aquitaine, maritime pine (INRA Pierroton), grapevine and peach tree (INRA Bordeaux) are investigated. The process consists in obtaining EST tags used to target genetical, physiological and molecular determinants of biological functions. To date, concerning maritime pine, 20,000 ESTs have been sequenced and we expect to reach 100,000 ESTs by the end of the year.

In order to perform ESTs analyses, a bioinformatics suite is being implemented by the CBiB in collaboration with different laboratories. This software permits to create a non-redundant set of sequences from the EST tags. Several informatics treatments are performed to group sequences belonging to the same gene in order to identify this gene. Three steps are subsequently used before obtaining the "annotated index".

  • trimming of sequences (remove remaining vector sequences, contaminating sequences) and masking of low-quality sequences 
  • grouping and clustering to reduce redundancy and group sequences belonging to the same gene 
  • functional annotation for the final identification.

The system we are developing includes third-part softwares (one of which is StackpackTM) and local developments.It is integrated from the sequencing process and automated upto functional annotation. We will shortly provide a public web access to our results and to the system which are presently restricted.


Figure 1. Steps of the treatment of the EST sequences 

 

 

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