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sheynkman-lab / biosurfer

"Surf" the biological network, from genome to transcriptome to proteome and back to gain insights into human disease biology.
MIT License
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ProteinAlignmentBlock should account for AA sequence matches #84

Open jsaquing opened 3 years ago

jsaquing commented 3 years ago

Right now match-type pblocks are generated only from match-type tblocks. There should be an additional "abacusing" step during the generation of pblocks that allows match-type pblocks to include codons that have been substituted at the transcript level but encode the same AA. This will become especially important for analyzing protein features such as domains.

jsaquing commented 3 years ago

schematic of different ways substitution pblocks could have matching subregions: 1