Computational methods in genome research

Abstract

Computational biology has revolutionized biological and medical research. In the last two decades, a large number of computer methods have been developed to analyze DNA, RNA and protein sequences. These computer methods are playing a vital role in extracting useful information from sequences of genomes. These computational methods have been developed by different academic groups all over the world to serve the biological community. The methods are available as stand alone programs or on-line web servers. Most of these software packages are available free for academicians (freeware). In this chapter, we have described the major computational methods available for biologists to extract information from sequences. This chapter covers computational methods f r i) genome annotation; ii) comparative genomics; iii) protein structure prediction; iv) functional classification of proteins; and v) identification of potential vaccine candidates. These software packages are not available from a single source so it is not easy for users to obtain the software of their interest. In order to overcome this problem, attempts have been made to collect and compile a list of free biological software programs that includes software at EMBL and Indiana University. A catalog of biological software (Biocatalog) is also available on the internet ( Rodriguez-Tome 1998 ). Recently, a repository of free software in biology has been created at Institute of Microbial Technology, Chandigarh, India which contains more than 800 free software packages.