Extracting clusters and alignment scores of members from FoldSeek Cluster (preferrably programmatically) #479
Description
Hello,
First I would like to thank you for the incredible work and congratulate you on the publications!
I am currently trying to set up a similarity network based on protein structures, with an enzyme of interest as a query. As such, I would like to extract the cluster members, alongside a metric like alignment score or e-value to use for the clustering. However, from the webserver I can seemingly only get the uniprot IDs of the cluster members, and from the API I can only seem to get an output with NCBI taxonomy IDs, without any identifier for cluster members or a score.
Is there any possibility to query the webserver in a way that allows for the extraction of all cluster members alongside the alignment scores that led to the formation of that cluster? I have seen that the full all vs all pairwise alignment file is also available, but due to the size of this file I am first looking at alternative solutions. I would be very interested to hear what your recommended approach would be, and thank you in advance.