#5056 closed enhancement (fixed)
Allow blastprotein command to use a UniProt name or id
Reported by: | Tom Goddard | Owned by: | Zach Pearson |
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Priority: | moderate | Milestone: | |
Component: | Sequence | Version: | |
Keywords: | Cc: | pett, Elaine Meng | |
Blocked By: | Blocking: | ||
Notify when closed: | Platform: | all | |
Project: | ChimeraX |
Description
Would be convenient if the blastprotein command could take as the first argument a uniprot name
blastprotein MELB_ECOLI
or uniprot id
blastprotein P02921
It could do a web query to fetch the sequence or just run command "open MELB_ECOLI from uniprot".
Change History (3)
comment:1 by , 3 years ago
Resolution: | → fixed |
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Status: | assigned → closed |
follow-up: 2 comment:2 by , 3 years ago
I'll look into making the alphafold search command not convert uniprot name to accession code if the blastprotein command is doing it.
follow-up: 3 comment:3 by , 3 years ago
The alphafold search command does not run the blastprotein command. Instead it creates a BlastProteinJob directly using the explicit sequence. So there is no code duplication to remove unless we want the alphafold search command to invoke the blastprotein command. I don't plan to do that.
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This was implemented today, but there is now a little bit of duplicated processing in the AlphaFold and blastprotein bundles. Still, I tested the AlphaFold search command and it is working.