Without seeing the image you are talking about its a crap shoot but here goes…
In AE on one layer you could draw a matte around the clouds you want the lightning (you spelled lighting but Im assuming you wanted lightning)
so the cloud is isolated.
On the next layer (below the first) copy the same clip.
Then sandwich in between these two layers another plain layer. On this one apply the AE flare effect. Animate the opacity and placementand blend it to taste.
Just one of many ways. And alternate would be to assign a glow to the middle layer which now is a dup of the other two . Animate the glow . Mask it if necessary.
Tom Daigon
PrP / After Effects Editor
http://www.hdshotsandcuts.com
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