Trypanosomatid EST: a neglected information resource regarding flagellated protozoa?

Expressed Sequence Tag (EST) sequence analysis rapidly gained widespread use and application for the discovery of gene transcripts in a variety of organisms (Adams et al. 1991). As of April 11, 2008, 51,391,051 ESTs entries were recorded in the dbEST NCBI (National Center of Biotechnology Information). Most of these (61%) are generated from laboratory models and economically important organisms (21 species; see Table I for the 10 most frequently sequenced organisms). ESTs have proven invaluable tools for accelerating the discovery of transcribed sequences in the genome and generating markers for genome mapping. Several bioinformatic methods for the analysis of ESTs at both small and large scales have been developed in the last 10 years. A thorough revision of these methods as well as a comprehensive analysis regarding the breadth of their applications for EST processing, quality sequence analysis and functional discovery has been published by Nagaraj et al. (2007). Accompanying this road map analysis is a guide through the world of EST bioinformatics tools available at http:// biolinfo.org/EST/. This guide contains an extensive list of software and methods. For the purpose of this opinion article, I am focusing on the Trypanosoma cruzi EST collection. This analysis may, in general terms, be applied to other trypanosomatids. To illustrate this opinion with examples, I have searched the T. cruzi EST dataset as described below. The full collection of T. cruzi ESTs in the dbESTGenBank NCBI was downloaded and screened for the presence of the spliced leader fragment at the 5’ end. After redundancy elimination, this EST set was aligned with ClustalX (Thompson et al. 1997) in order to identify genes with evidence of alternative trans-splicing. Each EST set was compared to genomic sequences available either in GenBank (www.ncbi.nlm.nih.gov) or GeneDB (www.GeneDB.org) to confirm the presence of poly-pyrimidine-rich regions and trans-splicing sites (AG dinucleotide). This procedure allowed the discarding of any artifacts from the cDNA libraries primed