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Hello,
I was hoping you may be able to clarify a COG annotation question. Apologies if this is a silly question I've just struggled to find an answer and I'm quite the amateur. I've used a pangenom…
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Hi,
The tool says that it can work with GFF3. But it only works with GTF. Can we get GFF3 support?
![image](https://github.com/user-attachments/assets/53e82137-3291-454e-b21f-762e2639b3d6)
Er…
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Now we get modifications from UniProt there are exact duplicates. We should filter them like we filter GO, with the PomBase annotations taking priority.
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Hi Gerry,
I get that Panstripe's main goal is to model the gene exchange rates, but would it be straightforward to get an idea of the function of the exchanged genes? I'm thinking of listing annota…
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- gene-disease annotations should be only for terms defined by the gene causing the disease (e.g ~type1; ...)
- these annotations should come from OMIM only
- the annotation should be brought in ONL…
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Consider adding more annotation information, depending on the direction we want to take CycleDash.
(Or allowing for plugins with this information.)
For example, @timodonnell talking about UCSC:
```…
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In annotations (gff3) files, what should we do about genes missing the Note attribute? The InterMine build process expects this attribute to exist.
Workaround for experimental ViciaMine: I added ";…
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* **PTHR ID & PTN node:**
GO:0003961 | O-acetylhomoserine aminocarboxypropyltransferase activity | IBA with PTN002887184 , S000004294 , CAL0000188058 , met17
* **Sequences with problematic a…
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I used the commands to create a reference for AnnotSV:
```
wget http://ftp.ensembl.org/pub/release-
111/gtf/homo_sapiens/Homo_sapiens.GRCh38.111.chr.gtf.gz
wget http://hgdownload.cse.ucsc.edu/ad…
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### Main steps for adding new genome and annotation collections
# Genus/species/collection names:
Haplotype 1:
- Cercis/canadensis/genomes/ISC453364.gnm3.GWXB
- Cercis/canadensis/annotations/IS…