Bioinformatic tools for identifying proteins with certain amino acid sequence motif

Question

[Jung-ho Kong]

Hi Thank you so much in advance.

I hope to know if there is any tool that identifies proteins that contain certain amino acid sequence. There is a list of 90 proteins and what I hope to find out is that if the proteins in the list contain amino acid sequence of 'KFERQ'.

Previously I had downloaded individual protein sequences via FASTA and looked if the protein sequence contain the amino acid sequence. Searching for the amino acid sequence individually for each proteins is just time consuming.

Thanks.

[Jean-Karim Heriche]

What's wrong using grep or writing a simple script ? e.g.:

grep 'KFERQ' *.fasta

[Joe]

BLAST with heavy mismatch penalties and no gaps if you want to query all the databases, otherwise I would do what Jean advised. You can search all your files in an instant.

Answer 1

[Jean-Karim Heriche]

Have a look at the ELM database.