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Novel computational tool for protein sequencing

Research Achievements

Novel computational tool for protein sequencing

Protein sequencing is a challenging and time-consuming experimental endeavor. However, recent advancements in peptide mass spectrometry have enabled the identification of protein sequences using a database of known proteins. These new methods fail for proteins such as alternative splice variants, mutated sequences, and antibodies, which are difficult to account for in a database of reasonable size. In many instances, a curated database of proteins may not be available for the organism of interest. Natalie Castellana, who is co-mentored by Vineet Bafna (Computer Science Engineering) and Steve Briggs (Biology), co-authored a paper entitled "Template Proteogenomics: sequencing whole proteins using an imperfect database" which presents a novel computational tool for protein sequencing in the presence of an incomplete or inaccurate protein database.