[BiO BB] Semantic meaning of N in genomic sequences

[Ryan Golhar]

I'm performing some analysis on different chromosomes of different
species and noticed some chromosomes contain spans of N.  Some of the
N's are of the same lengths, and others are of different lengths.

A span of Ns in the genomic sequence (as I understand it) could
represent 1 of 3 things:

1.  Region between two sytenous sequences on a contig/scaffold/etc with
unknown size and/or sequence
2.  Region on a contig of known size that is difficult to sequence
3.  Region on a contig of unknown size that is difficult to sequence

I'm trying to determine if certain spans of N represent any of the
categories above, and which one in particular.  Is there any standard
for how many N's should be in place to represent anything in particular?
How can you determine what a span on Ns represent?

Ryan

--
Ryan Golhar  -  golharam at umdnj.edu
The Informatics Institute of UMDNJ