A Variety Of Organisms And Genes Predicted Amino Acid Composition Analysis

Three parts are included in this paper. The first is the reannotation of the genome of Pyrobaculum aerophilum str. IM2. Firstly and most importantly, we found23new genes missed in the original annotation, by combining database search results of ORFs predicted by five genefinding programs, namely AMIGene, BASys, RAST, MicroScope and ZCURVE1.0. Among these new genes, five have significant similarities with function-known genes and the rest have significant similarities with hypothetical ORFs contained in other genomes. Secondly, the coding potentials of1645hypothetical ORFs were re-predicted by using33Z curve variables combined with Fisher linear discrimination method. With the accuracy at99.68%,25originally annotated hypothetical ORFs were recognized as non-coding by our method. And subsequent analysis provides further evidences supporting the result. Thirdly,80hypothetical ORFs were assigned with potential functions by using similarity search with BLAST program. Re-annotation of the genome will benefit related researches on this hyperthermophilic crenarchaeon. Also, the re-annotation procedure may be taken as a reference for other archaeal genomes.Target genes for new drugs that resisted Neisseria meningitides053442and other Neisseria were predicted in this paper. Potential drug targets genes included66new genes predicted by ZCURVE1.0,325essential genes predicted by DEG_match1.0,202highly expressed genes predicted by Codon W and128ones predicted with E (g) index, and225genes in7genomic islands predicted with Zcurve method. Only120potential drug target genes left after homologous search with genome of Neisseria bacteria, Homo sapien and beneficial bacteria. The next optimization step was to find out those potential drug target genes homologous with sequences collected in Drugbank and VFDB databases. Finally,18highly reliable drug target genes were found, and one of them was newly annotated gene, three of them were essential genes and three were genomic island genes and highly expressed genes. After prediction of subcellular location,6of the18genes were predicted to locate at out membrane. Drug targets prediction in this paper were comprehensive and could be taken as reference for drug targets in other genome.In the third Part we studied the relationship between tRNA gene usage and amino acid usage in17archaea,359bacteria and34eukaryote genomes. The co-variation relationship between the two was reported in this paper. The co-variation relationship is also influenced by the genome constitution components like GC content, genome size, tRNA gene copy numbers and others. But no significant signs that gene expression influences the relationship were shown.