Abstract
Biological informatics (BI) has emerged as one of the most important interdisciplinary fields in the last decade. Major research efforts in BI include nucleotide sequence and structure alignment, gene finding and genome assembly, gene expression and regulation, protein and RNA structure prediction, biological networks and pathway analysis, genome- wide association studies, computational proteomics and biomarker detection, molecular evolution and population genetics, to name a few. These efforts are often concurrent with the development of software tools for data analysis, leading to new discoveries in diverse areas of the biological sciences.
In this chapter, we present a case study in BI, focusing on locating non-coding RNAs in Drosophila genomes using software tools, in particular the Infernal package. Non-coding RNAs (ncRNAs) are functional RNA transcripts that are not messenger RNAs and therefore are not templates in protein biosynthesis. Recent experiments have shown that ncRNAs perform a wide range of cellular functions. In particular, RNA on the X-1 (roX1) plays an essential role in the dosage compensation system, which increases the transcription level on the X chromosome in Drosophila males (XY) with respect to that of females (XX). Experiments have shown roX1 functionality in some species of Drosophila whose genomes have been annotated. Our working hypothesis is that RNA transcripts of the roX1 genes across Drosophila species possess conserved secondary structures. Advances in genomic sequencing from twelve Drosophila species will contribute to support this hypothesis.