Good Morning:
Masking refers to marking areas of repeat sequence in the genome.
We use both RepeatMasker and TRF simple repeats to mark
areas of the genome. About %50 of the human genome is so marked.
See also:
http://genome.ucsc.edu/FAQ/FAQdownloads#download16
--Hiram
Pattle Pun wrote:
> ** High Priority **
>
> Dear Jennifer,
>
> Thanks for your quick response.
>
> I think my question is that I do not understand the difference/relation
> between "masking or unmasking" and lower/upper case designation in the
> alignments in your BLAT system. Please explain.
>
> Pattle.P.T.Pun, Ph.D.
> Professor of Biology,
> Wheaton College,
> Wheaton, IL 60187
> phone: 630-752-5303
> fax: 630-752-5996
> email: [email protected]
> http://www.wheaton.edu/Biology/faculty/ppp/index.html
>>>> Jennifer Jackson <[email protected]> 02/17/09 9:03 PM >>>
> Hello,
>
> For this linked alignment, the blue colored bases represent those that
> are in the alignment. This is unrelated to masking.
>
> For the previous alignment, when I said:
>
> "the "+" means that the data are compatible but differ (in this case by
> being soft-masked/unmasked between the query/target)"
>
> I mean that the "|" is the same as an exact match, same base, same state
> of masking.
>
> And that the "+" is also considered a match, but a different kind of
> match. Not the same as an exact match (above) because even though they
> are the same base (i.e. compatible, to be interpreted as a match) they
> differ in the state of masking (one is masked, the other unmasked).
>
> I hope this helps to clarify the data,
> Jennifer Jackson
> UCSC Genome Bioinformatics Group
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