TargetFinder and Annotator: a Simple Approach for Finding Full-length Target cDNAs and for Annotating EST Sequences

In a large scale EST (expressed sequence tag) or cDNA sequencing project, it is often desirable to know whether the ESTs identify genes of interest and whether the cloned cDNAs include intact coding regions (are of full-length). In this work, we present two Perl tools, TargetFinder and Annotator. TargetFinder automates the identification of full-length cDNAs from assembled EST sequences including singletons and contigs. Annotator is used to annotate ESTs and their assembled sequences by assigning a provisional function to each sequence and predicting whether or not they include intact coding regions. The programs use the output of BLASTX to predict the correct reading frame, search for a putative start codon, and predict whether a query sequence includes an intact ORF. In addition the programs also predict whether the sequence of the coding region of a cDNA clone or a contig is complete. Using our own Aspergillus niger EST data, TargetFinder rapidly and accurately found full-length target genes within a large set of assembled ESTs and Annotator functionally annotated the ESTs and their assembled sequences.