DNA sequencing and bioinformatics

DNA sequencing includes several methods and technologies that are used for determining the order of the nucleotide bases—adenine, guanine, cytosine, and thymine—in a molecule of DNA. The chain-termination method developed by Frederick Sanger and coworkers in 1977 at the University of Cambridge in England became the method of choice for DNA sequencing.

Once a DNA sequence has been obtained from an organism, it is stored in silico in digital format. In silico is used as an analogy to the Latin phrases in vivo, in vitro, and in situ, which are commonly used in biology. It means performed on computer. Usually the DNA sequences are stored in sequence databases that can be searched using a variety of methods. One of these methods is BLAST (Basic Local Alignment Search Tool), a registered trademark of the National Library of Medicine.

The application of computer science and information technology to the field of biology and medicine is called Bioinformatics. A renowned Genome Bioinformatics website is developed and maintained by the Genome Bioinformatics Group, a cross-departmental team within the Center for Biomolecular Science and Engineering (CBSE) at the University of California Santa Cruz (UCSC).

A sequence alignment is a way of arranging the sequences of DNA, RNA, or protein to identify regions of similarity that may be a consequence of functional, structural, or evolutionary relationships between the sequences. Aligned sequences are typically represented as rows within a matrix. Gaps are inserted between the residues so that identical or similar characters are aligned in successive columns.

A list of links to some biological databases and software tools is shown below :

  •  BLAST : Basic Local Alignment Search Tool
  • ENCODE : Encyclopedia of DNA Elements Consortium – an international collaboration of research groups funded by the National Human Genome Research Institute (NHGRI)
  • Neanderthaler Project : Neandertal Genome Analysis Consortium Tracks
  • Genome Browser : this program zooms and scrolls over chromosomes, showing the work of annotators worldwide
  • Gene Sorter : this program displays a sorted table of genes that are related to one another
  • Blat : this program quickly maps a sequence to the genome
  • Table Browser : this program retrieves data associated with a track in text format
  • Visi Gene : this program is a virtual microscope for viewing in situ images
  • Genome Graphs : this program is a tool for displaying genome-wide data sets
  • Mouse Genome Informatics : the international database resource for the laboratory mouse, providing integrated genetic, genomic, and biological data to facilitate the study of human health and disease