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In mass spectrometry based proteomics, protein homology leads to
many shared peptides within and between species. This complicates
taxonomic inference. inference. We introduce PepGM, a graphical model for taxonomic profiling of viral proteomes and metaproteomic datasets.
Using the graphical model, our approach computes statistically sound
scores for taxa based on peptide scores from a previous database
search, eliminating the need for commonly used heuristics. heuristics.
In mass spectrometry based proteomics, protein homology leads to
many shared peptides within and between species. This complicates
taxonomic inference. inference. We introduce PepGM, a graphical model for taxonomic profiling of viral proteomes and metaproteomic datasets.
Using the graphical model, our approach computes statistically sound
scores for taxa based on peptide scores from a previous database
search, eliminating the need for commonly used heuristics.
Results suggest a reduction in immune gene repertoires in termites and possible complementary expression between termite castes. With comparative genomics we will investigate the evolution of gene families related to immunity, try to understand where reductions and expansions take place and relate these changes to shifts in sociality and ecology. The role of TEs in expansions and contractions of immune gene families will be investigated. For these analyses, we propose to generate high quality, highly contiguous genomes of species from different levels of sociality, covering all major termite families. With comparative transcriptomics we will investigate the expression of immune genes in different castes. Via network analyses we will identify pathways indicated in differential immunity between castes and between species of different sociality levels. We will investigate how these pathways have been rewired along the transitions to higher levels of sociality and how, intra-specifically, they change between castes.