All of the split solutions using look-arounds that have been posted so far have problems coping with Ns at the beginning or end of the string. If you want to use split I think the simplest approach would be to combine it with grep and length, splitting on one or more Ns without any look-arounds.

$ perl -E '
> $seq = q{NNACGTNNNACGTNACGTNN};
> say for grep length, split m{N+}, $seq;'
ACGT
ACGT
ACGT
$

[download]

I hope this is of interest.

Cheers,

JohnGG

In reply to Re: Splitting only on internal pattern, not at start or end of string by johngg
in thread Splitting only on internal pattern, not at start or end of string by BiologySwede

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