Genomics and proteomics methods have witnessed a huge surge in the
recent decade. Provided the pace of data accumulation from several advanced
technologies such as next-generation sequencing, transcriptomics, ChipSeq and
quantitative proteomics, the parallel growth in the functional annotation is relatively
slow and needs continuous curation and analysis of existed data from repositories.
Nevertheless, the standard procedures of functional annotations of proteins which were
based on classical data sets, need to be revised in light of advanced and more
comprehensive data. In fact, most omics technologies are now integrating and their
merger can provide a much realistic and holistic picture of any biochemical and
molecular scenario provided the data handling and curation is performed on cellular
and molecular principles. A number of genomes and proteomes have been functionally
annotated in the past; microbial genomes offer a better opportunity with less complex
models. Nevertheless, microbes are among one of the most common causatives of
pathogenic diseases and their diagnosis, treatment is limited by available information
of proteins and their functions. Previously annotated hypothetical functions to proteins
are likely to change in some cases therefore a number of research groups have
attempted to re-annotate the microbial genomes with newer data-sets and new tools.
Re-annotation of Mycobacterium tuberculosis was one such example. Besides
pathogenic microbes, emerging trends in various useful microbes sequencing have
shown a tremendous increase in information on human microflora and remain a highly
prospective area in biology. Systems biology lies at the interphase of biology,
mathematics and computational biology and involves a holistic approach to visualize a
biological phenomenon. This chapter describes the basic principles involved in the
functional annotation of hypothetical proteins in light of emerging datasets and tools.
Besides the suggestions on improving standard pipelines, it also presents a summary of
recently annotated microbial genomes and future prospects of involving systems
biology in the functional annotation for improved quality and output.
Keywords: Annotations, Microbial proteins, Network enrichment, Systems biology.
