Searching for conserved short motifs

Question

[Saulius Lukauskas]

Is there some off-the-shelf tool that would allow me to input a short motif that I know is conserved in a particular family of proteins, let's say KKKRNNDKK or something (purely making it up) and perhaps find other proteins that have a very similar motif which is also conserved among their family or phylogenetic tree?

Answer 1

[cyril-cros]

I don't know your experience in bioinformatics, but searching for patterns is usually done with the Meme suite

The Motif Scanning / Meme enrichment sections are what interests you. It can give hits in a protein sequence database, but finding similar families is a bit harder. You can use the PANTHER (evolution) or GO (function) databases. Look also at the tools mentioned there: Finding differential enrichment of known motif in gene set