Question: Bioinformatic tools for identifying proteins with certain amino acid sequence motif
gravatar for Jung-ho Kong
3.1 years ago by
Jung-ho Kong0 wrote:

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.


sequence • 1.2k views
ADD COMMENTlink modified 3.1 years ago by Jean-Karim Heriche23k • written 3.1 years ago by Jung-ho Kong0

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

grep 'KFERQ' *.fasta
ADD REPLYlink written 3.1 years ago by Jean-Karim Heriche23k

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.

ADD REPLYlink modified 3.1 years ago • written 3.1 years ago by Joe18k
gravatar for Jean-Karim Heriche
3.1 years ago by
EMBL Heidelberg, Germany
Jean-Karim Heriche23k wrote:

Have a look at the ELM database.

ADD COMMENTlink written 3.1 years ago by Jean-Karim Heriche23k
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