A web Based Software for Synonymous Codon Usage Indices

Abstract

The genetic codes have degeneracy. Most of the amino acids are encoded by more than one codon. Codons encoding the same amino acid are called synonymous codons. The patterns of codon usage vary considerably among organisms, and also among genes from the same genome. This phenomenon is known as codon biasness. Various factors contribute to codon usage biasness like gene expression level, %G+C composition, GC skewness, transcriptional selection. These factors form a pattern called synonymous codon usage pattern which explains the causes of variations present in the genes. Several indices have been used to measure the degree of non-random usage of synonymous codons in a gene. With the exponential increase in the volume of the sequence information, detailed statistical analysis of codon usage is highly desired. Complete analysis of codon usage for gene expression studies requires using many softwares and standard statistical packages for visual representation of data. Some of packages for codon usage analysis are stand alone and are not easily accessible. So, comprehensive web based software for codon usage analysis is highly required by researchers. This paper describes a web based software for analyzing the non-random usage of synonymous codons using various indices developed by researchers. This software is developed using Java, JSP, Apache Tomcat Server and MS-Access. The software will be highly useful for biologists, statisticians and computer scientist involved in biological research.