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Hi there!
Thanks for this great tool - it is my first time using it (also beginner with protein structures)
I created by own prostT5 database from 345 AA seqs by doing this:
```
foldseek dat…
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## Bug Description
I tried to run it on the following fasta file it gives me this error:
```fasta
>seq-2
MKKKKKKKLKKLKKKLKKKLKKKKKLLLLLLLLKKKKKKK
>seq-9
MKKKIKKIKKKIEKKKKKKLKKLKKKKKKKKLLLLLLLLL
…
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Hello dear Alphapulldown developers.
I am trying to set up the colabfold part for alphapulldown. I got my *.a3m files in a directory and I run rename_colab_search_a3m.py to get more meaningful filena…
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Dear Pauline,
I have been trying to use make-SIFT-db-all.pl to create a database. It all seems to be going well, and files are being created in the directories singleRecords, fasta and subst (the …
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The `msa_hmm` step combines two alignments into one file. Both the ingroup and the outgroup are processed separately to figure out the revcom orientation and do the alignment. The files are then simpl…
rvosa updated
3 months ago
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I'm interested in developing consensus COI reference sequences for major groups in BOLD:
[BOLD](https://www.boldsystems.org/index.php/TaxBrowser_Home)
I'm guessing I can parse the database infor…
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hello,
Could u help me why this appered?thanks
thinkstation# dnadiff sequence.fasta query.fasta
Building alignments
Filtering alignments
Extracting alignment coordinates
Analyzing SNPs
ERROR…
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Hi @mnshgl0110 and everyone :)
I'm sorry if this is a really obvious question, I'm new to programming and haven't used Syri before.
I am getting this error code when I try to run Syri:
"Runnin…
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## Expected Behavior
I am trying to build a custom database from my own fasta file by (1) clustering all protein sequences using `mmseqs` and then (2) following the steps of [https://github.com/soedi…
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I am looking at the beam search decoding script for RNN-T models in espnet1 https://github.com/espnet/espnet/blob/c4aba12f9de93cb021e869a2ecce61da18b0c484/espnet/nets/beam_search_transducer.py#L247. I…