Contig Files upper and small case nucleotides

Question

[waqasnayab]

Hi,

I merged different assemblies of different sequencing platforms bh minimus2.

The output of resulting merged contig fasta file is some what like this:

TTAGAAGTAGGCCGGTATGTGAGTGGGACACCTCnCGAGATGTAGGCCTGCGTGnTTGCT
GTGGCGTCGAAATGAACGGTTTAGGAGGCnATGGGCCGGACTAGCCAGGATAATGACCCG
GGACACCACGCCGTCGAGGAACGCACGACCGTCGCTGCnTCTAnAnAGATCGCCAGCGCT
TTATACTGGGCGGCnACCCCTCGGTCAGAGGATCAGGCTTGTGCTGGAGCTACCCTCAGG
CATCTGAGCGGTGATACTTATTTGGGGAATAATGAAAATCGGCTTAAGTTCnnGCCCCA

Are they maksed region in lower case letters (n) ? Can I proceed further with Gene prediction step or Should I have to do something, like remove n or replce with N?

Regards,

Waqasuddin Khan.