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* **PTHR ID & PTN node:**
GO:0000030 | mannosyltransferase activity | IBA with S000000557 , PTN002003922 | contributes_to | GO_REF:0000033
* **Sequences with problematic annotation (ID + gene/pr…
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I've been developing a metagenomic/metatranscriptomics software suite called VEBA (https://github.com/jolespin/veba) that natively handles eukaryotic binning of metagenome-assembled genomes and exon-a…
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Hi,
is it possible to use `phylotaR` also for retrieving orthologous protein sequences (using all-vs.-all blastp searches) from Genbank/NCBI?
Many thanks in advance for your help!
Jan
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> http://dx.doi.org/10.1371/journal.pone.0141287
>
> **Motivation:** We introduce a new representation and feature extraction method for biological sequences. Named bio-vectors (BioVec) to refer to…
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For some reason there was an IndexError when running the method below, but since the variable `codon_alignment` was never initialized there was a UnboundLocalError raised as well claiming: _local vari…
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Hi!
I'm having some trouble understanding where this can come from.
I tried to align a sequence with HMMER and filter on the e-value at 1e-05.
With HMMER, I have this result in the domtblout:
```
…
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(RFAA1) [2200012187@hr-6-6-login RoseTTAFold-All-Atom]$ python -m rf2aa.run_inference --config-name protein
/gpfs/share/home/2200012187/mambaforge/envs/RFAA1/lib/python3.10/site-packages/hydra/_inter…
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Hi,
I finally managed to get ufcg running with `--set NUC`, only to realise that it then only uses ITS.
Why isn't it using all the `core` genes in `NUC` mode as it does in `PRO` mode?
Can that …
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Hi,
I want to know if foldseek can output multiple structural alignment generated using 3Di as aligned 3Di alphabet sequences in Fasta format and not aligned amino acid sequences of the proteins.…