Remove redundant nucleotide sequences in a FASTA file containing ambiguous N

Question

[wang9ting]

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!

[Ram]

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

[wang9ting]

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

[Ram]

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

Answer 1

[Pierre Lindenbaum]

my java solution:

[wang9ting]

Many thanks! It works well.