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?
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written
by
Saulius Lukauskas
1 answer
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
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written
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cyril-cros
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