Mastering Perl for Bioinformatics

Foreword

If you can’t do bioinformatics, you can’t do biology, and Perl is the biologist’s favorite language for doing bioinformatics. The genomics revolution has so altered the landscape of biology that almost anyone who works at the bench now spends much of his time at the computer as well, browsing through the large online databases of genes, proteins, interactions and published papers. For example, the availability of an (almost) complete catalog of all the genes in human has fundamentally changed how anyone involved in genetic research works. Traditionally, a biologist would spend days thinking out the strategy for identifying a gene and months working in the lab cloning and screening to get his hands on it. Now he spends days thinking out the appropriate strategy for mining the gene from a genome database, seconds executing the query, and another few minutes ordering the appropriate clone from the resource center. The availability of genomes from many species and phyla makes it possible to apply comparative genomics techniques to the problems of identifying functionally significant portions of proteins or finding the genes responsible for a species’ or strains distinguishing traits.

Parallel revolutions are occurring in neurobiology, in which new imaging techniques allow functional changes in the nervous systems of higher organisms to be observed in situ; in clinical research, where the computer database is rapidly replacing the paper chart; and even in botany, where herbaria ...