Genes, Genomes and Genomics ©2008Global Science Books Computational Genome Analysis Using The G-language System

Computational genome analysis requires sophisticated workflows, seamlessly uniting multiple tools and algorithms. In order to maximize the productivity of genomics research with bioinformatics, a computational framework that allows rapid integration of available resources is desirable. G-language Genome Analysis Environment is a generic open-source workbench for this purpose, with the aim to: 1) construct an integrated analysis and development environment for bioinformatics, 2) systematically accumulate and implement existing algorithms and data, and to 3) aid the construction of analysis workflows. This system provides over 200 analysis methods for genome informatics and systems biology, with programmable interfaces, an interactive command-line shell, and a graphical user interface. Here we review the methods and algorithms implemented in this system especially focusing on genome informatics analysis, including methods for the identification of sequences with significant information content using information theory, observation of nucleotide composition and genomic compositional asymmetry, calculation of codon bias measures and prediction of gene expression levels, and statistical analysis of short oligomers such as short tandem repeats and palindromes. Since these methods are combined with several other applications and algorithms to produce a workflow in genome informatics research for studying specific biological questions, we als