EUGENE swMATH ID: 9286 Software Authors: Schiex, Thomas; Moisan, Annick; Rouzé, Pierre Description: EUGÈNE: An eukaryotic gene finder that combines several sources of evidence. In this paper, we describe the basis of EUGÈNE, a gene finder for eukaryotic organisms applied to Arabidopsis thaliana. The specificity of EUGÈNE, compared to existing gene finding software, is that EUGÈNE has been designed to combine the output of several information sources, including output of other software or user information. To achieve this, a weighted directed acyclic graph (DAG) is built in such a way that a shortest feasible path in this graph represents the most likely gene structure of the underlying DNA sequence. The usual simple Bellman linear time shortest path algorithm for DAG has been replaced by a shortest path with constraints algorithm. The constraints express minimum length of introns or intergenic regions. The specificity of the constraints leads to an algorithm which is still linear both in time and space. EUGÈNE effectiveness has been assessed on Araset, a recent dataset of Arabidopsis thaliana sequences used to evaluate several existing gene finding software. It appears that, despite its simplicity, EUGÈNE gives results which compare very favourably to existing software. We try to analyse the reasons of these results. Homepage: http://link.springer.com/chapter/10.1007/3-540-45727-5_10 Related Software: GENEVESTIGATOR; TAHMMAnnot; mclust; NTAP; TileMap; R Cited in: 2 Publications all top 5 Cited by 8 Authors 1 Aubourg, Sébastien 1 Bérard, Caroline 1 Brunaud, Véronique 1 Martin-Magniette, Marie-Laure 1 Moisan, Annick 1 Robin, Stéphane 1 Rouzé, Pierre 1 Schiex, Thomas Cited in 1 Serial 1 Statistical Applications in Genetics and Molecular Biology Cited in 2 Fields 2 Biology and other natural sciences (92-XX) 1 Probability theory and stochastic processes (60-XX) Citations by Year