From March 14, 2019 to April 13, 2019
During this one month secondment at the MMS laboratory of Le Mans University, we aimed to study transposable elements in Haslea ostrearia genome using bioinformatics software and in silico tools.
Genome assembly of non-model organisms is usually not at chromosomal level and highly fragmented. This fragmentation is recognized to be, in part, the result of a bad assembly of the transposable elements (TEs) copies, increasing the difficulty to detect and annotate them. In this context, a new bioinformatics pipeline named PiRATE for detect, classify and annotate TEs of non-model organisms. PiRATE combines multiple analysis packages representing all the major approaches for TE detection.
The detection of complete TE sequences, bearing recognizable conserved domains or specific motifs, allows facilitating the classification step. The classification step of PiRATE is optimized for algal genomes.
A further bioinformatics exploration should be carried out in perspective of this secondment, in order to succeed in optimally identifying the transposable elements for the diatom Haslea ostrearia.
