How to extract a protein sequence?

Question

[ioer0417]

Hello.

How to extract a protein sequence?

I have two files.

< file 1. complete_protein.fasta >

protein_1

DCXSTEISLFHEIWLF

protein_2

AJFOWIDJLSIDJFJ

protein_3

DJFLWIDJFLSKDJFL

protein_4

DKSJFLEISJDKJF

< file 2. only proteinID.fasta >

protein_1

protein_4

I need about sequence in file2. That sequence have in file1.

So, I tried "diff" command, but result is I don't want data.

How to extract??

[GenoMax]

Answers here should work as well: Extract fasta sequences from a file using a list in another file.

Answer 1

[antonioggsousa]

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

[ioer0417]

Thank you so much!

Your answer helped me a lot.