PiRATE: a Pipeline to Retrieve and Annotate Transposable Elements

To date, genome assembly of non-model organisms is usually not at chromosomal level and is higly 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, we designed a new bioinformatics pipeline named PiRATE for detect, classify and annotate TEs of non-model organisms. We optimized its detection step by gathering every existing TE detection approaches. The goal is to promote the detection of complete TE sequences of every TE families. The detection of complete TE sequences, bearing recognizable conserved domains or specific motifs, allows to facilitate the classification step. The classification step of PiRATE has been improved for algal genomes. Each tools used by PiRATE are automated into a stand-alone Galaxy. This PiRATE-Galaxy can be used through a Virtual Machine, which can be download below. This PiRATE-Galaxy is a suitable and flexible platform to study TEs in the genome of every organisms. Please dowload and read the tutorial.

Additional Info

Field Value
Creator Nicolas, Daccord;Nathalie, Casse;Véronique, Jamilloux;Grégory, Carrier;Jérémy, Berthelier;Bruno, Saint-jean
Contact Seanoe
DOI http://dx.doi.org/10.17882/51795
Discipline Oceanography
MetaDataAccess http://www.seanoe.org/oai/OAIHandler?verb=GetRecord&metadataPrefix=oai_dc&identifier=oai:seanoe.org:51795
PublicationYear 2018
Publisher Seanoe
Rights CC-BY-NC