Bioinformatics : decoding the genome

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Extracting the fundamental genomic sequence from the DNA From Genome to Sequence : Biology in the early 21st century has been radically transformed by the availability of the full genome sequences of an ever increasing number of life forms, from bacteria to major crop plants and to humans. The lecture will concentrate on the computational challenges associated with the production, storage and analysis of genome sequence data, with an emphasis on mammalian genomes. The quality and usability of genome sequences is increasingly conditioned by the careful integration of strategies for data collection and computational analysis, from the construction of maps and libraries to the assembly of raw data into sequence contigs and chromosome-sized scaffolds. Once the sequence is assembled, a major challenge is the mapping of biologically relevant information onto this sequence: promoters, introns and exons of protein-encoding genes, regulatory elements, functional RNAs, pseudogenes, transposons, etc. The methodological approaches and data requirements for genome annotation will be discussed, as well as user interfaces for exploring genomes. Polymorphic variation in the human genome and susceptibility to disease : One of the main features revealed by the completion of the human genome is the large amount of polymorphic sequence variation present in human populations, such that on average any two chromosomes differ every 600 - 800 base pairs. The majority of these sequence variants are Single Nucleotide Polymorphisms (SNPs), although other types of polymorphisms exist. So far around 5 million SNPs have been validated, and an international consortium has been set-up to characterize the main features of human variation in different populations (www.hapmap.org). Although most of the sequence variation in the human genome is thought to be neutral, a fraction of it is known to have functional consequences, for instance, modifying the activity/function of a protein or affecting the…