Genscan for Arabidopsis is a valuable tool for predicting sponge coding sequences

Although the first sponge genome project has already started releasing completed sequences, only a very small number of annotated sponge genomic sequences has so far been published. In addition, no gene-prediction software optimised for sponges is available yet. In the present paper, we present the performance of Arabidopsis-optimised Genscan as tested on sponge genes. All genes whose genomic and complete CDS sequences are deposited in the NCBI nucleotide database were retrieved and used as the test set. The 18 test genes are composed of 114 coding exons. The sensitivity and specificity, respectively, of all exons were predicted with 83.3% and 79.2%, internal exons with 88.5% and 80.2%, donor with 93.8% and 85.7%, acceptor with 89.6% and 78.9%, initiation with 94.4% and 85%, and termination sites with 72.2% and 81.3%. The results are compared with prediction results obtained with Genscan for vertebrates and GeneMark.hmm ES-3.0 for Arabidopsis. The surprising finding is that although the animals are the source of sequences, the best results (more than 80% accuracy in predicting complete exons) were obtained by Genscan optimised for a plant A. thaliana. Although the sample is small, the results lead to the conclusion that Genscan for Arabidopsis is a valuable tool for predicting coding sequences in sponges and could be of great help in annotating sponge genes.