Hi,

If you are working with linux distribution you can try the following command-line:

grep -f target_protein.txt -A1 protein_file.txt | sed '/--/d'  > retrieved_protein.txt

This takes the protein_file.txt file that contains the same content that you posted above:

protein_1
DCXSTEISLFHEIWLF
protein_2
AJFOWIDJLSIDJFJ
protein_3  
DJFLWIDJFLSKDJFL
protein_4
DKSJFLEISJDKJF
  

And the file target_protein.txt that contains the target protein names that you want to retrieve from the file above:

protein_1
protein_4
  

The output of protein target sequences of interest is saved in retrieved_protein.txt, that looks like:

protein_1
DCXSTEISLFHEIWLF
protein_4
DKSJFLEISJDKJF
  

I hope this helps,

António