Design of an Optoelectronic Biomolecular Scanning System using Smart VCSEL and Photodetector Arrays

摘要

Biological databases, unlike general-purpose databases, have a unique data format and organization that require specialized searching techniques. Protein and DNA sequences (biosequences) are stored as character strings that can be several thousand characters (also called bases) long. The character sets for protein and DNA strings contain 20 and 5 distinct characters, respectively. Biomolecular scanning (BMS) involves taking a query biosequence and comparing it to every biosequence in the database to identify a subset of biosequences that are similar to the original string. The seemingly simple operation of string comparison becomes an extremely tedious computation because of the sheer size of the database (e.g. GenBank currently contains more than 2 * 10~9 bases in 2,838,000 sequence records) and the need to search for similarities that may include character insertions, deletions, and substitutions in addition to exact matches. BMS is the basic operation for a number of significantly more complex tasks in molecular systematics that include multiple biosequence alignment and phylogenetic tree reconstruction. In both cases, a large number of iterations of the basic search algorithm must be performed.