[Genome] caps letters genomic sequences

[Hiram Clawson]

Good Morning Vesko:

This depends upon how you obtained the sequence.

If you used the blue navigation bar at the top of
most pages in the genome browser labeled "DNA" that
sequence is masked via the RepeatMasker track as
indicated by lower case letters.  This depends upon
which option you selected in that output screen.

If you obtained the sequence via table browser operations,
again, it depends upon what options you selected in
the output screen.  Gene tracks can be obtained with
CDS in upper case.

If you are looking at the sequence in the fasta files
from hgdownload, that sequence is masked with RepeatMasker
and TRF simple repeats of period less than 12 as explained
in the README in the directory where you obtained
the sequence.

If there is some other mechanism by which you obtained this
sequence and it was not obvious what was being delivered,
please let us know so we can get it documented properly
to avoid future confusion.

Thank you for your assistance,

--Hiram


Vesselin Baev wrote:
> Dear All,
> I have a sequences from PanTro2. some of them include caps letters -
> are the caps CDS/exon regions?
> so if I want to discard seqs that correspond to proteins, can I delete
> seqs that include caps letters?
> 
> Vesko