File:PAG2011 P820 Triannot.pdf

Triannot: A User Friendly Web Interface For Structural And Functional Automatic Annotation Of Plant Genomes

Poster presented by Philippe Leroy at PAG 2011.

Abstract

Philippe Leroy, Nicolas Guilhot, Hiroaki Sakai, Aurélien Bernard, Frederic Choulet, Céline Pelegrin, Sébastien Reboux, Timothée Flutre, Naoki Amano, Michael Seidel, Hajime Ohyanagi, Michael Alaux, Hisataka Numa, Tsuyoshi Tanaka, Klaus Mayer, Takeshi Itoh, Hadi Quesneville, Catherine Feuillet

Structural and functional annotations are essential for connecting genome sequence to biology. To achieve a systematic and comprehensive annotation of the wheat genome (17 Gb), a pipeline called TriAnnot has been developed under the umbrella of the IWGSC. TriAnnot provides the international scientific community with an online friendly user interface, highly customizable and written in PERL object. Its architecture is divided into three main panels. The first panel comprises modules for repeats and Transposable Elements (TEs) masking and annotation. The second panel is dedicated to protein-coding genes structural and functional annotation. The whole process is based on ab initio gene prediction programs and similarity search against transcript databanks. The confidence of gene models is assessed through a grade level, visualized using GBrowse with a color code. The functional annotation follows the IWGSC annotation guide line. Finally, the third panel searches for biological evidences as well as other biological targets such as tRNAs after masking TEs from Panel 1 and Gene Models from Panel 2 (optional) thereby facilitating the identification of biological features based on comparative genomics. Annotations are graphically displayed under the GBrowse viewer (default analysis only), and GFF and EMBL output files can also be downloaded. The accuracy (sensitivity- Sn, specificity - Sp) of the TriAnnot V2.1 gene modeling has been evaluated (Eval - Washington University) using 18 Mb of manually curated sequences from the wheat genome (Choulet et al. 2010.), and compared with four other available international pipelines (MIPS, FPGP, RiceGAAS, DNA subway).