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I'm experiencing a crash. Any help would be much appreciated.
```
%prokka -v
prokka 1.12-beta
% prokka --prefix groups --cpus 0 --norrna --notrna --outdir prokka_knot --force contigs.name.fasta
[snip…
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A reviewer of the cilia GO ontology manuscript has requested an additional component term as part of the bacterial flagellum. @paolaroncaglia, @JohnvanDam, and I need to work on this promptly to meet…
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Hi,
I have installed the latest version of Prokka and I get the following error:
[19:53:29] Could not run command: tbl2asn -V b -a r10k -l paired-ends -M n -N 1 -y 'Annotated using prokka 1.14.6 …
avonm updated
4 years ago
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For the cell ontology, the following proteins would help define neutrophils
Neutrophil collagenase P22894
Neutrophil elastase P08246
Matrix metalloproteinase-9 P14780
Amil…
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Hi @amandamackie
I am looking at LPS transport. There are 2 similar function terms annotated by EcoCyc:
- GO:0015221 lipopolysaccharide transmembrane transporter activity
- GO:0015437 lipopolysa…
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very bad
GO:0001871 pattern binding
Interacting selectively and non-covalently with a repeating or polymeric structure, such as a polysaccharide or peptidoglycan. PMID:12072369 PMID:122259…
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While putting in a new complex term for @bmeldal, I noticed that there is some inconsistency with the location of the xrefs to IntAct IDs. There are over 200 hits for the string "IntAct:EBI", sometime…
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Dear Torsten,
I run the Prokka’s version 1.13, but, the .gbf file was deleted. I installed Prokka on Ubuntu using the command "brew install brewsci/bio/prokka". I thought something was wrong with m…
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In the simulation data, there is a reaction `R15-RXN-MET/CPD-479//CPD-479/MET.25.` with stoichiometry `{u'CPD-479[c]': 0, u'MET[c]': 0}`. I don't know why this is the case, but it's the only instance…
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In higher eukaryotes this family is a likely endomembrane acetyl A transporter. I don't know if it is a proton symporter, but I don't think this can be transferred from E.coli. It seems unlikely