Natural sequence code representations for compression and rapid searching of human-genome style databases
Barry Robson, P. J. Greaney · Computer applications in the biosciences · 1992
Numeric descriptions ('bio-informatic descriptions') of amino acid residues have been developed which will be of value whenever the quality and quantity of information in very large (i.e. 'human genome style') gene and protein sequences is to be compared or manipulated. These codes are as natural as possible by our criteria (the same principles could be used in revision of the criteria). In particular, in storing and searching large amounts of sequence data, natural codes--which relate to the properties of amino acids--can be combined with existing fast-search algorithms but introduce several advantages. The code can be assigned such that sub-selection of bits leads to compressed databases with residues defined less specifically, by classes of properties. The most compressed representation leads to the specification of a residue as polar or non-polar, while the most extended representation used at present also allows specification of, for example, glyco-asparagine and phosphoserine. Preliminary studies on both a supercomputer and smaller machines suggest a 'worst-case' speeding of approximately 4.5-fold. For more intelligent searching, coding extensions mixed with the basic sequence data give the sequence data some of the character of a computer program.