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Remove redundant nucleotide sequences in a FASTA file containing ambiguous N

Is there any tool for removing redundant sequences in the scenario where "N" stands for A or C or G or T?

For example:

>seq1
ACNTACNT
>seq2
ACGTACGT
>seq3
ACGTACCT
>seq4
ACTTACAT
>seq5
TCGTACTT
>seq6
TCGTACTT
...

seq2, seq3, and seq4 should be removed because they are redundant sequences of seq1. And seq6 should be removed because it's a redundant sequence of seq5.

The function could be used for all IUPAC ambiguity codes, but now I'm only interested in having "N" and A,C,G,T in sequences.

Thanks!

fasta redundant
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updated by Ram Ram • written by wang9ting • wang9ting

Have you tried searching online? This question has been addressed numerous times.

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written by Ram Ram

Thanks for reaching out. Yes, I have tried searching, but could not find a good solution. Pierre Lindenbaum's code works well.

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written by wang9ting • wang9ting

Ah, you have Ns - sorry I didn't see that before.

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written by Ram Ram

1 answer

my java solution:

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written by Pierre Lindenbaum Pierre Lindenbaum

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