MMseqsTemplate

A Easy-to use Template for mmseqs search and cluster. Reduce identity between protein sequences.

Installation

Just install mmseqs in the official website. Remember the path of your mmseqs binary, this will be used in our script later.

Usage

Check the scripts in usage folder and replace the template with your own paths:

1. mmseqs binary path (eg. /usr/local/mmseqs/bin/mmseqs)
2. input fasta path (eg. /root/project/MMseqsTemplate/data/protein.fasta)
3. output fasta path (eg. /root/project/MMseqsTemplate/data/protein_rep50.fasta)

Then run the scripts directly.

Case 1: save the cluster center only

run usage/mmseq_cluster.sh

• input: fasta file
• output: fasta file (smaller)

Case 2: save the cluster result and the groups

run usage/mmseq_group.sh

• input: fasta file
• output: fasta-like file (larger) eg. A fasta-like file may be like this:

  >sequence96
  >sequence96
  AVPVAVWLVSALAMGAGVAGG
  >sequence192
  AVPVAVWLVSALAMGAGMAGG
  >sequence165
  >sequence1
  >sequence1
  FLGFLLGVGSAIASGVAVSKV
  >sequence0
  FLGFLLGVGSAIASGTAVSKV
  >sequence72
  FLGFLLGIGSAIASGVAVSKV
  

Case 3: filter similar sequence

run usage/mmseq_search.sh

• input: 2 fasta files
• output: list of the filtered sequence names