TY - JOUR AU - Blanquart, Samuel AU - Varré, Jean-Stéphane AU - Guertin, Paul AU - Perrin, Amandine AU - Bergeron, Anne AU - Swenson, Krister M. PY - 2016 DA - 2016/11/11 TI - Assisted transcriptome reconstruction and splicing orthology JO - BMC Genomics SP - 786 VL - 17 IS - 10 AB - Transcriptome reconstruction, defined as the identification of all protein isoforms that may be expressed by a gene, is a notably difficult computational task. With real data, the best methods based on RNA-seq data identify barely 21 % of the expressed transcripts. While waiting for algorithms and sequencing techniques to improve — as has been strongly suggested in the literature — it is important to evaluate assisted transcriptome prediction; this is the question of how alternative transcription in one species performs as a predictor of protein isoforms in another relatively close species. Most evidence-based gene predictors use transcripts from other species to annotate a genome, but the predictive power of procedures that use exclusively transcripts from external species has never been quantified. The cornerstone of such an evaluation is the correct identification of pairs of transcripts with the same splicing patterns, called splicing orthologs. SN - 1471-2164 UR - https://doi.org/10.1186/s12864-016-3103-6 DO - 10.1186/s12864-016-3103-6 ID - Blanquart2016 ER -