foldseek

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link target ids to real name

1

Hi, Is there a way to request NCBI or Uniprot accessions and/or the functions of the target proteins using foldseek api ? with the python command : result = get('https://search.foldseek.com/api/result/'...

lalalagartija

add --format-output for both html and table

2

(Not a bug, just asking for a new feature :) ) Hi, I started using the tool, which looks very useful and efficient! thanks for all the hard work It...

rothita

foldseek all-vs-all mode fails?

2

I'm running a simple easy-search for a folder against itself (to get the pairwise tm-scores) using the following: foldseek easy-search --alignment-type 1 --tmscore-threshold 0.0 /some/folder /some/folder aln.m8 tmpFolder /some/folder has...

kwanUm

Dataset problem

2

## Context I find some problems in the link you give about Benchmark data and Foldseek databases: http://wwwuser.gwdg.de/~compbiol/foldseek/ 1. [pdb.tar.gz](http://wwwuser.gwdg.de/~compbiol/foldseek/pdb.tar.gz) and [scp40pdb.tar.gz](http://wwwuser.gwdg.de/~compbiol/foldseek/scp40pdb.tar.gz). It seems that they are just the same....

maovshao

Error: target createdb died

9

While running foldseek easy-search I ran into the following error. ##installed foldseek conda install -c conda-forge -c bioconda foldseek ##installed database foldseek databases Alphafold/Proteome afdb tmp ##try to run easysearch...

calvincicha

ERROR "Format code alntmscore does not exist."

2

When I run the command line proposed for "Rescore aligments using TMscore" (with my own intputs data"): **foldseek easy-search example/ example/ aln tmp --format-output query,target,alntmscore,u,t** I am getting the error...

matiascarletti

Brief description of output columns?

3

Thanks a lot for this wonderful tool. Unfortunately, I couldn't find a brief description of the output format. The output I have downloaded misses column headers. So, I don't know...

rezahay

Web Service Fails/Hangs when Using TM-align mode

3

When searching any protein on the web server (https://search.foldseek.com/) I continue to get failures when using the TM-align mode. I tried this with a number of proteins and loaded accessions.

kthurimella

Cannot create databases

7

## Expected Behavior `foldseek databases PDB pdb tmp` should setup PDB database ## Current Behavior Returns: gzip: stdin: not in gzip format tar: Child returned status 1 tar: Error is...

jabard89

Generate alignments/give rotation&translation matrix

12

Hi, It is a very nice software and extremely fast, thank you! One question: would it be possible that the server provides the superimposed structures and/or the translation-rotation matrix for...

gezmi