All-vs-all search on clustering result for visualisation in Cytoscape

[eric-jm-lang]

Hi,

Appologies if this question has already been answered, but I do not seem to find it in the manual and within the entered Issues.

I have run a clustering and would like to visualise the clusters in Cytoscape. As far as I know I have to run an all-vs-all search on my clustering results (and converting the results toa BLAST tabulated output) .

However, I cannot find a way to do it directly from the clustering results using something like:

mmseqs cluster DB DB_clu tmp
mmseqs search DB_clu DB_clu DB_clu_allvsall tmp

as I get the following error:

Input database "DB_clu " has the wrong type (Clustering)
Allowed input:
- Index
- Nucleotide
- Profile
- Aminoacid

Instead, it seems that I have to convert the clustered database to a normal database, i.e.

mmseqs cluster DB DB_clu tmp
mmseqs createseqfiledb DB DB_clu DB_clu_seq 
mmseqs result2flat DB DB DB_clu_seq DB_clu_seq.fasta
mmseqs createdb DB_clu_seq.fasta DB_clu_seq_DB
mmseqs search  DB_clu_seq_DB  DB_clu_seq_DB DB_clu_allvsall tmp

Is it the best way to do it (as it seems a little convoluted)? Or is there a way to do a all-vs-all search directly from the clustered results which would be easier/faster?

Many thanks in advance

[wenyuhaokikika]

I got same error,how to fix? or fake_prefilter can not support for mmseqs search?