Automatic Prediction and Annotation

Catherine Mathé (1) , Christophe Dunand (1)

1 Dynamique et Evolution des Parois cellulaires végétales

In the last few decades, the explosion of genomic projects has produced huge sets of predicted genes and annotated sequences. The prediction of a gene structure can be defined as the capacity to determine the start and the stop of the gene as well as the positions of introns, if present. Despite the number of performant gene prediction programs combining ab initio and homology-based approaches (Mathe et al., 2002; Hoff and Stanke, 2015), the rate of mis-predicted genes is not negligible and can be due to several factors (Scalzitti et al., 2020). For example, unusually long introns, short exons or long genes can generate incomplete or partially predicted gene structure; short intergenic regions can lead to gene fusion; DNA sequencing errors (nucleotide deletions or insertions) introducing frameshifts can affect predictions; non-canonical splice sites, overlapping genes and genes located within introns are also a source of erroneous predictions. [...]

Mots clés: protein annotation; gene prediction; gene family; mis-prediction; mis-annotation

Domaines: Biologie végétale

Catherine Mathé, Christophe Dunand. Automatic Prediction and Annotation: There Are Strong Biases for Multigenic Families. Frontiers in Genetics, 2021, 12, pp.697477. ⟨10.3389/fgene.2021.697477⟩. ⟨hal-03460651⟩