Extracting the pattern not matching

[Mug_4]

Hi there,

I have a list of sequence id and I am trying to extract the sequences from the proteome of the organism using these ids. I used the grep command with -w and -f to find out the sequences and got some of the sequences. Further, I want to extract the remaining sequences of my list from uniprot. For this I am trying to identify the sequence ids from my listfile which I could not find in the proteome set. How can I do this using grep/awk/sed commands or any other oneliner?

Thanks

[dpryan]

Well, you'd need to show the exact format of everything to get a one-liner, so I can't help you there (at the moment at least). However, what it sounds like you want is an inverted match grep (usually grep -v). You can likely combine that in with your previous grep command to get the output that you want.

[Mug_4]

Thanks. grep -v is not the solution for me. I have a list file like
list.txt that contains the multiple strings as
AVD
HJK
DFT
XXT
MNZ
LRB
..

I have a protein sequence file from uniprot. I used grep -wi -f list.txt uniprot.fasta > out

out contains the sequences that are matched with the pattern in the file list.txt. What I exactly want the strings from list.txt not matched with uniprot.fasta

Well, you'd need to show the exact format of everything to get a one-liner, so I can't help you there (at the moment at least). However, what it sounds like you want is an inverted match grep (usually grep -v). You can likely combine that in with your previous grep command to get the output that you want.

[Apexy]

Try:
grep -wiv -f list.txt uniprot.fasta > out