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The Alliance of Genome Resources (AGR) is a consortium of the most highly-used model organisms (mouse, rat, worm, fly, zebrafish, yeast), and they have released their own set of ortholog assignments a…
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In https://github.com/biothings/biothings_explorer/issues/792, knowledge_level / agent_type (KL/AT) info was added to all x-bte operations for Service-Provider-only KPs. There were multiple cases wher…
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Hi,
I am new to Eggnog-Mapper and barely have experience on using Python. Previously I attempted to install it on Windows computer but failed to run it for some problems that I had no idea how to…
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if A is orthologous to Y
and
B is orthologous to Y
then A and B are paralogs
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The Translator consortium wants knowledge_level / agent_type (KL/AT) edge-attributes added to all edges.
The format for the edge-attributes is something like this:
```
{
"attribute_type_id…
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Hi,
I'm looking at the and product of CAT, run only using TransMap and excluding the indel classification `r.extend(find_indels(tx, psl, aln_mode))`.
I'm now trying to build a table of orthologs…
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- also make sure we should be using GO_REF:0000096 for both human->mouse and rat->mouse ortholog annotations?
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Currently for MGI, we're filtering out all ISO annotation lines from GPAD. We now want to allow ISO lines to be translated in model if that ISO line has `Assigned_by=MGI`.
This shouldn't affect oth…
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Hello - I would like to obtain a similarity metric between the pair of orthologue proteins detected by orthofinder or, even better, all the pairwise similarities in the input set of sequences. Is this…
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Hi,
I used `download_eggnog_data.py` to download the insect hmmer search file.(`python download_eggnog_data.py -H -d 2759 -y --data_dir /home/data/eggnog/annotation/hmmer/50557` )
I then got a folde…