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Harsha Gowda

Harsha Gowda IOB, India

Genomes and transcriptomes of a number of organisms have been sequenced in the recent years. One of the major goals of genome sequencing efforts is to provide an accurate assembly and annotation of all the genomic features including protein coding genes. Annotation of protein coding genes has been largely carried out using a combination of transcriptome data and gene prediction programs. However, our studies using a novel approach called proteogenomics has revealed inherent limitations of these widely used approaches. Proteogenomics is an emerging field that uses mass spectrometry based proteomics data to directly identify protein coding regions in the genome and transcriptome. Using this approach, we have identified novel protein coding regions in annotated genomes of both prokaryotic and eukaryotic organisms. We have also demonstrated that some of the annotated pseudogenes and non-coding RNAs code for proteins thus challenging the conventional ways in which these annotations are being carried out. These observations make a compelling case for employing proteomics to annotate genomes and identify novel proteins that have not been discovered till date.

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