Research paradigms in modern biology are shifting from a single gene to a genome-wide scale. Two major contributions toward this new trend are large-scale genome sequencing and bioinformatics. Recently, bioinformatics has emerged as a new science field that provides computational tools for collecting and maintaining complex biological data. Along with an exponential accumulation of sequence data, many bioinformatics software and algorithms have been developed to assist in genome scale analyses. A comprehensive knowledge of these tools can help not only to understand gene functions and genome organizations, but also to provide an opportunity to develop new tools that can answer many biological questions.