Addition of Human and Chimp genome sequences to the growing collection of complete eukaryotic genome sequences has provided a boost to comparative genomic approaches for identification of genes and their biological function.Even as the task of assigning atleast a single function to each and every gene in the human genome through bioinformatics and experimental validation will occupy us for several years, the upcoming challenge is to predict multiple functions of single genes using comparative methods.The interplay of regulatory elements and nucleosome positioning signals along the chromosomal is the next step in understanding transcriptional control.The presences of thousand of noncoding transcripts pose a new challenge for their functional annotation and assigning role to these transcripts in the context of human biology. As more and more proteomics and transcriptomics data are being generated for the same set of tissues and conditions, mapping the gap between these two data sets pose the next level of understanding of post transcriptional regulation in the human genome.Understanding the emerging role of newly discovered conserved miRNA sequences in the translational control in cancer tissues and host pathogen interaction needs development of novel bioinformatics tools.Ultimately development of bioinformatics tools for identification of relevant protein protein interaction map will enable us to decipher the association of SNPs to complex disorders in a functional context.