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How to remove ambiguous amino acid code containing sequences from a Fasta file?

I have a fasta file with 396 protein sequences (the header in one line and amino acid codes in several lines). Some of these sequences contain ambiguous or exceptional amino acid codes (e.g., B, J, O, U, Z, X, -- ). I want to remove sequences containing such code and generate a new fasta file. How I can do this in the Ubuntu terminal? Thanks in advance.

sequence
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updated by Pierre Lindenbaum Pierre Lindenbaum • written by Anisur Rahman • Anisur Rahman

not sure what your goal is but simply removing those ambiguous AA from the sequence is likely not the best idea (as you will change/destroy the overall context of that protein).

Replacing the ambiguous ones with X for instance should work . Normally none the the tools dealing with protein sequences should have a problem with X as an "aminoacid" .

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written by lieven.sterck lieven.sterck

I want to remove the whole sequence which contain ambiguous AA code.

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written by Anisur Rahman • Anisur Rahman

I will use these sequences for population conservancy analysis in the immune epitope database. ambiguous AA containing sequence cause error during this analysis. I don't know replacing ambiguous with X will work or not, I didn't try this approach. Ok please, also suggest me how I can replace ambiguous AA with X?

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written by Anisur Rahman • Anisur Rahman

building on the one liner Pierre Lindenbaum provided below :

sed '/^[^>]/s/[BJOUZ]/X/g' in.fa  > out.fa

this will replace all occurrences of B, J, O, U, Z with an X .

removing the whole sequence makes sense as well but will require different code.

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written by lieven.sterck lieven.sterck

Thank you for your explanation. I am trying this code also. Please, suggest me the code to remove the whole sequence.

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written by Anisur Rahman • Anisur Rahman

2 answers

if you don't mind ending up a with a fasta file where the sequence is on a single line you could give the following a try:

perl -pe '$. > 1 and /^>/ ? print "\n" : chomp' <your_file> | paste - - | grep -v "\t.*[BJOUZ]" | tr "\t" "\n"

this will first put all sequences on single line perl -pe '$. > 1 and /^>/ ? print "\n" : chomp' , then put both header and sequence on a single line (tab separated) paste - - , then remove the lines containing the chars you don't want grep -v "\t.*[BJOUZ]" , and finally split header and sequence back to two lines tr "\t" "\n"

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written by lieven.sterck lieven.sterck 
sed '/^[^>]/s/[BJOUZX]//g' in.fa  > out.fa
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written by Pierre Lindenbaum Pierre Lindenbaum

Sorry to say, this is not working. The code supposed to exclude some sequences in the output file. But in output file number of sequences remain the same 396. I am not sure whether the code is removing the whole sequence or only the ambiguous amino acids.

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written by Anisur Rahman • Anisur Rahman

this code will remove all ambiguous aminoacids from the sequence but will indeed not remove the sequence.

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written by lieven.sterck lieven.sterck

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