"N"s in DNA sequence data

[rdu]

I found there're many "N"s in a initial DNA genome sequence data, like:

CTGAAATCACTACTTTCCTTGTTAGGCTCGGCGCATGTGTTAAGTAGNNN
NTTATANNCNGNNNAGNATTTATNNNNNNNNCTTNNNNNNCGGTTATATG

What's the explanation for it? I took BLASTX allignment, no error messages popped up, then how BLAST treats them? Thanks.

[apratap]

Hi rdu

I see these messy N's always in the Illumina data. I think it could mean variety of different things but this is just my interpretation. Mianly I think when the base caller is not able to decipher which nucleotide to call it leaves "N" behind. If you see bunch of N a the end it could relate to falling quality. However if you see a long stretch in the middle, it could also mean complexity in that genomic region.

HTH
-Abhi

[rdu]

Hi apratap,

Thank you. Your anwser sounds reasonable. If I know some related futher, will also share with you. Have a nice day.

[aloliveira]

Hello,

The Blast ignore that sequences, there is a lower-complexity filter by default on BLAST to avoid miss-called bases or masked bases (normally N or X correspondingly). You can turn-off that parameter if you want.

Best regards,
André.