Analysis of string-searching algorithms on biological sequence databases

Abstract

String-searching algorithms are used to find the occurrences of a search string in a given text. The advent of digital computers has stimulated the development of string-searching algorithms for various applications. Here, we report the performance of all string-searching algorithms on widely used biological sequence databases containing the building blocks of nucleotides (in the case of nucleic acid sequence database) and amino acids (in the case of protein sequence database). The biological sequence databases used in the present study are Protein Information Resource (PIR), SWISSPROT, and amino acid and nucleotide sequences of all genomes available in the genome database. The average time taken for different search-string lengths considered for study has been taken as an indicator of performance for comparison between various methods.