Finding the approximate location of short read genome sequences by comparing them to an already available closely related organism's complete genome sequence is a challenging research issue. Predicting intron locations in the short form of mRNA called Expressed Sequence Tags (ESTs) and the variability of intron lengths are the major challenges. More specifically, finding the intron positions in an EST sequence by comparing it with a reference genome sequence is a time consuming task, as currently it is done manually.

In my thesis, I designed a pipeline that can predict the intron positions in ESTs of non-model organisms. Initially, I compared the ESTs to the closest completely sequenced genome. The pipeline then finds the alignment of the ESTs, the reference genome sequence, and the coding region of the gene (known as Coding DNA Sequence or CDS) from the reference genome.