[BiO BB] Semantic meaning of N in genomic sequences

pmr at ebi.ac.uk pmr at ebi.ac.uk
Thu Dec 15 05:26:27 EST 2005

Hi Ryan,

> 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?

Hope you are not relying opnly on a FASTA format file of sequences :-)

"If all else fails, read the documentation" - in other words, you shoudl
be able to find out most of what you need from the full EMBL or GenBank
entry (worth checking both formats to see which is easiest to parse).

Even if you are using a FASTA file, you can retrieve the full entry to
check when you need more information.

Of course some of us would 'cheat' by using the ID and species to guess :-)

Hope that helps a bit,

Peter Rice

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