Find NLS in list of proteins.

Question

[qmarulfiz]

Like the question said. I am clueless.

I have list of NLS (nuclear localization signal ) and list of proteins. I am interested to see whether any of my list proteins have my listed NLS.

[qmarulfiz]

I just did simple test using grep function in R. But there must be available R package or bioresources or something outthere that I don't know.

Answer 1

[Joe]

Use a proper NLS/signal peptide prediction tool, e.g.: https://www.frontiersin.org/articles/10.3389/fgene.2020.607812/full

A grep-like approach will only really work if you are looking for very specific canonical peptides, or you'll have to get your hands dirty with fuzzy matching and regex to capture variance.

[qmarulfiz]

Thanks, I receive a specific list of NLS from my supervisor and he want to see whether these NLS exist in our list of proteins. Just heard the word NLS first time yesterday and I even have to google it. I happen to be the only one who knows a little bit of R in the lab so that's why thinking of grepl.

[Joe]

If you are looking for specific exact matches, that approach will work but I imagine you will need to do more like fuzzy matching.