The Analysis Of Bacterial Genomes And The Integration Of The Relevant Network Resources

With rapid progress of genome sequencing projects, a large number of genomes have been completed. It is now an urgent task to analyze the compositions in the genomic sequences. The nucleotide composition, described by the G+C content, has the wide variation across different bacterial genomes, which affected the composition of genes and proteins in the species. Meanwhile, the nucleotide composition in the genes is constrained to maintain the structure and function of proteins. It is very important for the relationship between genomic GC content and protein composition to understand the natural selection, mutation and microbial evolution.The sequences of1732bacterial genomes have been analyzed. It has been shown that the four bases are not evenly distributed at three codon positions. With the variation of GC content in genomes, the GC content at the third codon faster vary than those at the first and second codon positions. The contents of base A and G is higher, while the base T is low at the first codon position. In contrast, the G content is lower, and base T content is high, and slowly change with variation of GC content of genomes. The GC contents of genomes influence codon usage and amino acid compositions in protein coding sequences, however, amino acid compositions in proteins are modulated by base bias at three codon positions, which arise from structural and functional constraints. In addition, the hydrophobic amino acids in the all genomes are studied. Although the amino acid compositions in proteins are affected by the GC contents in genomes, the total content of hydrophobic amino acids change changes very little. It means that the content of the amino acids with specific property is constrained to maintain the protein the structure and function, when the GC contents in genomes change.In addition, a database and web interface of bioinformatics has been constructed based on the LAMP technique. The database contains the predicting results of replication origins in1250bacterial genomes provided by other student. A web server on identification of the first exons in eukaryotic genes is available at the web site. The database and web server can be freely accessed at http://10.1.25.220/bioinformatics/.