Storage and Matching Technique in Genomic Sequences for Approximate Motif Searching
Krishnarajanagar G. Srinivasa, H. S. Shashidhara · 2008
Sequence retrieval serves as a preprocess for a number of other processes including motif discovery, in which obtained sequences are scored against a consensus before being recognized as a motif. This depends on the way sequences are stored prior to retrieval. The usage of two bits for representing genomic characters is optimal storage wise, however does not provide any details regarding length of repetitive characters or other details of positional significance. The intent of the paper is to showcase an alternative storage technique for the sequence and its corresponding retrieval technique. We represent our technique with the use of integers for clarity of understanding. With the bit equivalent of the integers used in actual representation we could minimize storage complexity significantly. We give a clear picture of the requirements of a storage technique from a motif discovery perspective before showcasing our proposal.