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Provide the sequons and label for these highlighting templates #1532

Closed ReneRanzinger closed 5 hours ago

ReneRanzinger commented 1 month ago
ubhuiyan commented 1 month ago

Kate/Urnisha: Create mapping file based off of data Mike provides for misc folder.

rykahsay commented 1 month ago

@ubhuiyan ... any update on this?

katewarner commented 4 weeks ago

Here are the consensus sequences we found. @sujeetvkulkarni you may want to check these with @mtiemeyer0919 to make sure they are correct:

C-Mannosylation WXXW WXXC WXXWXXW WXXWXXWXXC

O-glucosylation CXSX(P/A)C CXNTXGSFXC

O-fucosylation CXXXX(S/T)C CXX(S/T)C

sujeetvkulkarni commented 3 weeks ago

@katewarner all other consensus sequences are found in https://www.ncbi.nlm.nih.gov/books/NBK579906/ except WXXWXXW (C-Mannosylation). What is the source of WXXWXXW (C-Mannosylation)?

katewarner commented 3 weeks ago

@sujeetvkulkarni It was from this paper: https://febs.onlinelibrary.wiley.com/doi/10.1111/febs.16265

rykahsay commented 2 weeks ago

@ubhuiyan ... where is the mapping file under the misc?

ubhuiyan commented 2 weeks ago

@rykahsay To my understanding, Sujeet had conducted his own research on consensus sequences and has already applied them to the front end. Kate has provided the sequences we found in this ticket for Sujeet to compare with his findings. I don't think she created a file in the misc folder for this given Sujeet has already been working on this.

Would you like for this mapping to also be present within our misc folder?

ubhuiyan commented 6 days ago

@rykahsay I have provided this mapping in misc/consensus_sequon_mapping.json. Please let me know if you'd like me to change anything.

rykahsay commented 2 days ago

@sujeetvkulkarni

Release specific URL for the file is: https://data.glygen.org/ln2releases/data/v-2.6.1/misc/consensus_sequon_mapping.json

After we push to prd, you can also use this URL: https://data.glygen.org/ln2releases/data/current/misc/consensus_sequon_mapping.json

sujeetvkulkarni commented 5 hours ago

@rykahsay We have referred these consensus sequences but a copy in frontend will be used to display and highlight protein sequences. Closing this ticket. Adding label informative for future reference.