I searched my pdb against dali server and found around 300 similar sequences in the result. After removing the redundant sequences, I am left with 50 sequences. Now I want to take only representative sequences from them.. is there any way to do it.. The dali server only show similarity with respect to my sequence..is there any way to show sequence similarity of each sequence relative to each other??
If you have the Sequences in fasta format, you can either run all-against-all alignment yourself using any sequence pair alignment tool. You can also use outputs from CD-HIT, to analyze the similarities.
You can also make use of the RCSB PDB site, sequence identity filter. Advance search with the list of PDBs and use filter (never tried myself).
You may try something like BLASTClust:
https://toolkit.tuebingen.mpg.de/blastclust
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