Our goal is to identify P. infestans genes expressed in planta through mining of publicly available ESTs corresponding to Solanaceae challenged with P. infestans cDNA libraries in compatible and incompatible interactions. To our knowledge, Randall et al. and Oh et al. carried out the only Metoclopramide hydrochloride hydrate studies that have used cDNA interaction libraries to focus on the pathogen��s gene expression in planta. Randall et al. included ca. 5,000 ESTs also included in this study and Oh et al. screened an interaction library for RXLR discovery and further Ardisiacrispin-A testing in planta. Our approach allowed us to find interesting genes, including different kinds of effector genes, as candidates for testing in the laboratory. Moreover, we were able to assign putative functions to novel sequences that may provide further understanding of plant�Coomycete pathosystems. This study attempts to extract genes from cDNA libraries expressed from the P. infestans transcriptome during attack on the host, using a combination of available resources and an innovative bioinformatics approach. First, our raw data consisted of all the sequences available to date from transcriptomic studies of Solanaceae Phytophthora interactions. Secondly, we took advantage of the most recent release of the P. infestans genome to separate pathogen from host sequences. Thirdly, the annotation process was exhaustive, using similarity approaches with a curated database and other small databases that contained characterized genes involved in pathogenesis, improving the efficiency of the whole annotation. A total of the initial unitigs assembly from interaction library of ESTs had a hit against the infestans genome. We knew that P. infestans sequences were present in the challenged libraries but we did not know whether there was a representative number to analyze the gene expression of P. infestans. In previous studies, the estimation of ����contaminating���� pathogen sequences was based on GC content. In view of the broad range of GC contents in the P. infestans CDS analyzed, it is clearly difficult to separate sequences belonging to host and pathogen merely by GC content.