Study of the Relationship between Mus musculus Protein Sequences and Their Biological Functions

The central challenge in post-genomic era is to characterize the biological functions of newly discovered proteins. Sequence similarity based approaches infer protein functions based on the homology between proteins. We present the similarity relationship between protein sequences and their functions for mouse (Mus musculus) proteome in the context of gene ontology (GO) slim. The similarity between protein sequences is computed using a measure based on the BLAST alignment scores. The similarity between protein functions is characterized using GO terms. We present the sequence similarity distributions at different levels of the GO tree. The similarities of protein sequences in GO groups residing on different branches of the GO tree are shown. Our results indicate that proteins with similar amino acid sequences tend to have similar biological functions. The posterior probabilities for correct function predictions were also computed. The result reveals certain limitations of the function prediction approaches that are solely based on sequence similarities.