Whole Genome Annotation: In Silico Analysis

After a genome is assembled, the next step is genomic annotation, which can generate data that will allow various types of research of the model organism. Complete DNA sequences of the organism are then mapped in areas pertinent to the research objectives. In this chapter, we explore relevant ongoing research on genes and consider the gene as a basic mapping unit. Gene prediction is the first hurdle we come across to begin the extensive and intensive work demonstrated in first item, which deals with assembly of the genome. Gene prediction can be made with computational techniques for recognizing gene sequences, including stop codons and the initial portions of nucleotide sequences; it involves empirical rules concerning minimum coding sequences (CDS's) and is limited due to overlapping sequences coding forward and reverse. Finishing gene prediction step by a computer initiates the functional annotation stage. Functional annotation, item 3, can be done initially by computer, using similarity in sequence alignment. However, no software is capable of generating a functional annotation without many false positive results, since conserved protein domains with varied functions make gene sequence alignment difficult. In this case, after automatic annotation, the predicted genes need to be revised manually. In manual curation, item 4, an expert can more accurately locate frameshifts in the DNA strand. Depending on the number of errors found, genomic annotation may be postponed, requiring a return to the previous stage of genome assembly. In manual curation, the principal contributions are usually correction of the start codon position, gene name, gene product and, finally, identification of frameshifts. When functional annotation is completed, the genome should subsequently be submitted. It occurs after the assembly and annotation steps making the data generated available in public-access databanks. Submission is a pre-requisite for publication in scientific journals. Another advantage of genome publication in public-access sites is that it permits use of various genome analysis tools. For example, searches for genomic plasticity, pangenomic study, exported antigens and evaluation of innate and adaptive immune responses. The pangenome approach, item 5, concepts of species can be used as a filter for targeting candidates for vaccines, diagnostic kits and drug development. For drug development, the