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Automated annotation of protein function is challenging. As the number of sequenced genomes rapidly grows, the overwhelming majority of protein products can only be annotated computationally. If computational predictions are to be relied upon, it is crucial that the accuracy of these methods be high. Here we report the results from the first large-scale(More)
BACKGROUND Advancements in function prediction algorithms are enabling large scale computational annotation for newly sequenced genomes. With the increase in the number of functionally well characterized proteins it has been observed that there are many proteins involved in more than one function. These proteins characterized as moonlighting proteins show(More)
MOTIVATION Importance of accurate automatic protein function prediction is ever increasing in the face of a large number of newly sequenced genomes and proteomics data that are awaiting biological interpretation. Conventional methods have focused on high sequence similarity-based annotation transfer which relies on the concept of homology. However, many(More)
Protein function prediction is a central problem in bioinformatics, increasing in importance recently due to the rapid accumulation of biological data awaiting interpretation. Sequence data represents the bulk of this new stock and is the obvious target for consideration as input, as newly sequenced organisms often lack any other type of biological(More)
The structural genomics projects have been accumulating an increasing number of protein structures, many of which remain functionally unknown. In parallel effort to experimental methods, computational methods are expected to make a significant contribution for functional elucidation of such proteins. However, conventional computational methods that transfer(More)
Biological interpretation of large scale omics data, such as protein-protein interaction data and microarray gene expression data, requires that the function of many genes in a data set is annotated or predicted. Here the predicted function for a gene does not necessarily have to be a detailed biochemical function; a broad class of function, or(More)
Investigation of protein gene function is a central question in molecular biology, biochemistry , and genetics. Because genes evolved from the same ancestral gene retain similarity in their function in most cases, finding known genes which have sufficient sequence similarity is a powerful way for predicting function. In this chapter we review computational(More)
Large scale genome sequencing technologies are increasing the abundance of experimental data which requires functional characterization. There is a continually widening gap between the mounting numbers of available genomes and completeness of their annotations, which makes it impractical to manually curate the genomes for function information. To handle(More)
BACKGROUND A new paradigm of biological investigation takes advantage of technologies that produce large high throughput datasets, including genome sequences, interactions of proteins, and gene expression. The ability of biologists to analyze and interpret such data relies on functional annotation of the included proteins, but even in highly characterized(More)
MOTIVATION Burgeoning sequencing technologies have generated massive amounts of genomic and proteomic data. Annotating the functions of proteins identified in this data has become a big and crucial problem. Various computational methods have been developed to infer the protein functions based on either the sequences or domains of proteins. The existing(More)