Use or abuse of bioinformatic tools: a response to Samach

In a recent paper, we described for the first time the effects of fruit on the expression of putative homologues of genes involved in flowering pathways. It was our aim to provide insight into the molecular mechanisms underlying alternate bearing in citrus. However, a bioinformatics-based critique of our and other related papers has been given by Samach in the preceding Viewpoint article in this issue of Annals of Botany. The use of certain bioinformatic tools in a context of structural rather than functional genomics can cast doubts about the veracity of a large amount of data published in recent years. In this response, the contentions raised by Samach are analysed, and rebuttals of his criticisms are presented.