ABSTRACT
Proteomics is concerned with the large-scale study of proteins. Beyond structural and functional analysis of individual proteins, proteomics research seeks to characterize the proteome of an organism in different cells and under different conditions and identify the molecular counterparts each protein interacts with. Sequence data is the most abundant type of data on proteins. Functional analysis of proteins is greatly enhanced by applying advanced algorithms that utilize the information in groups of homologous proteins. The goal of protein classification is to organize proteins into functional classes. Protein classification is extremely useful for function and structure analysis and is especially important for large-scale annotation efforts such as those that follow the large-scale sequencing projects. Higher level organization of proteins can also be studied by applying embedding techniques and mapping the protein space into real-normed spaces. This mapping not only facilitates the application of advanced data analysis tools.
