Consensus Motif

Question

[prs]

I have a MSA of amino acid sequences, and I want to generate a consensus motif sequence. For example, given four sequences: 1. ALVKLISG, 2. AIVHESAT, 3. CHVRDLSC, and 4. CPVESTIS, the desired motif output would be [AC]-x-V-X(4)-{ED}. I have tried tools like MEME and Jalview, but their outputs don't align with this format. Is there any tool, script, or method available that can directly produce such a consensus motif? I am open to command-line tools, scripts, or web-based solutions. Any suggestions would be appreciated. Thank you!

Answer 1

[Mensur Dlakic]

There is a web tool, but not sure it will work with the short sequences you have:

https://www.ebi.ac.uk/jdispatcher/pfa/pratt

There is an ancient version of the command-line tool:

https://ftp.ebi.ac.uk/pub/software/unix/