A strategy for high throughput microarray oligo probe design using 454 and sanger sequencing data of Eisenia fetida expressed sequence tags

High density oligonucleotide probe arrays have increasingly become an important tool in genomics studies. However, the lack of full genome sequences for many non-genomics model organisms has hampered researchers to pursue relevant ecological, toxicological, and other non-fundamental genomics questions. Historically, researchers have sequenced ESTs in the organism of interest prior to or in the absence of genome sequencing. Recent technological advances such as massively parallel pyrosequencing (454 sequencing) have provided ultra high throughput opportunities to sequence millions of bases in a few hours. Nevertheless, the sequence reads produced by the next generation sequencing technologies are relatively short and needs to be assembled into longer contigs, which created new challenges for probe design. Ideally, one oligo probe should target one unique gene or gene product (e.g., transcript). In the absence of genome sequence, one strategy is to target every unique transcript sequence while reduce the number of unique sequences (and costs of arrays) through bioinformatic analysis and experimental testing. Here we report a case study and demonstrate how this strategy was applied in the design of a transcriptome-wide oligo array for a non-gneomics model organisms Eisenia fetida.