[Next-Generation Sequencing Book]
  • [Photo] Gary Van Domselaar • December 4, 2000
    "High-throughput (HT) sequencing, microarray screening and protein expression profiling technologies drive discovery efforts in today's genomics and proteomics laboratories. These tools allow researchers to generate massive amounts of data, at a rate orders of magnitude greater than scientists ever anticipated. Initiatives to sequence entire genomes have resulted in single data sets ranging in size from 1.8 million nucleotides (Haemophilus influenza genome) to more than 3 billion (human genome)--a single microarray assay can easily produce information on thousands of genes, and a temporal protein expression profile may capture a data picture of 6,000 proteins.1

    It's what you do with the data that counts, however, and that's where bioinformatics takes over. Researchers in bioinformatics are dedicated to the development of applications that can store, compare, and analyze the voluminous quantities of data generated by the use of new technologies.

    One of the original functions of bioinformatics was to provide a mechanism to compare a query DNA or protein sequence against all sequences in a database. Several comparison algorithms have provided some successful and powerful computational applications,2 such as Smith-Waterman, FASTA, and BLAST. Early on, query sequences or sets of query sequences were relatively small, ranging from a few to 10,000 nucleotides, and 10- to 1,000-sequence query sets. Because of the proliferation and improvement of HT sequencing technologies, it is now common to find query sequences with 10,000 nucleotides and data sets containing up to 1 million sequences.

    The kinds of data developed and the methods for processing and analysis also have changed. Previously, small-scale DNA sequencing projects would perhaps generate 100 sequences (usually 50-400 nucleotides) that could be assembled relatively easily into a contiguous DNA sequence (a contig). Today, contig assembly may involve 1 million sequences with up to 5,000 nucleotides. The burgeoning fields of proteomics and microarray technologies provide another degree of complexity, adding multidimensional information to the biological data cornucopia. "

    Complete Article (requires 'free' registration):
    http://www.the-scientist.com/yr2000/nov/profile_001127.html

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