<p>Is there a way to search all human or mouse protein sequences for a short (~5 amino acids) degenerate amino acid sequence?</p>

You can do this easily by installing the FAST: Fast Analysis of Sequences Toolbox ([publication][1])([github][2]).

You can install it by using this command (only use sudo if you need to):

    (sudo) perl -MCPAN -e 'install FAST'

You will also need the fasta files containing human and mouse proteins. You can get these from NCBI.

Lets say that the sequences you are looking for are `ASNNF`, `ASNLF`, or `ASNKF`. To search for this you can use fasgrep which is a utility of FAST:

    fasgrep -is "ASN[NLK]F" <fasta-file-proteins>

This will return sequences that have either `ASNNF`, `ASNLF`, or `ASNKF`.

 [1]: http://journal.frontiersin.org/article/10.3389/fgene.2015.00172/abstract
 [2]: https://github.com/tlawrence3/FAST