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Hi,
My environment does not have enough RAM to run queries against the full `afdb` so I have been using `afdb50` instead. Searching against this database works perfectly well. However, after the in…
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I cannot find much information on how to view or process .m8 files. Please advise?
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Hello foldseek developer,
I'm trying to cluster protein based on structure. Apparently, the input file should be in PDB format, i used the mmseqs2 to creat db:
$ cat extracted_proteome.faa | mmseq…
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* version 1.0.4 on Linux 20.04, conda build
* What I did
```
source ${PATH_ACTIVATE}/activate ufcg
for file in ${INPUT}/*.fna;
do
if [ ! -d "./tmp" ]
then
mkdir ./tmp
…
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[extract-3di_textprinted.txt](https://github.com/samsledje/D-SCRIPT/files/12311823/extract-3di_textprinted.txt)
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Hello! I am currently trying to utilize the `genomad annotate` module to annotate a .fna file of Megahit assembled contigs. After downloading the database and attaching a unique identifier to each .fn…
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Hi, I'm using the following commands to get the alignments and taxonomic annotation, with translation table 6:
```
mmseqs search \
mmseqs-query-db/MK5a \
/media/bioinf/Data/EukProt_DB/comb…
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Is there documentation of the spec for SAM format used by `mmseqs`? I have aligned a bunch of protein sequences (both query and target are proteins) that resulted in >7.5M alignments and
* all of th…
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## Expected Behavior
* Create multiple sequence alignment FASTA (or .a3m) file from `mmseqs easy-search`.
* I can see how to convert a resulting DB to `.m8` but I'd like to convert in the other dire…
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## Main Issue
Dear mmseqs team,
I am a fairly new user of your software and have run into some unexpected behavior which I am unable to resolve. I am attempting to cluster a database of eukaryot…