[Genome] Can I get percent identities or similar scores from the conservation plots?

[Brooke Rhead]

Hello Mitchell,

You could use BLAT (the BLAST-Like Alignment Tool) to align sequences 
from another species to the human genome; BLAT will output a percent 
identity for the alignment.  Instructions for using BLAT are here:

http://genome.ucsc.edu/goldenPath/help/hgTracksHelp.html#BLATAlign

Note the limitations on using BLAT:
"Only DNA sequences of 25,000 or fewer bases and protein or translated 
sequence of 10000 or fewer letters will be processed. Up to 25 sequences 
can be submitted at the same time. The total limit for multiple sequence 
submissions is 50,000 bases or 25,000 letters."

If you have further questions, or if this method is not a good solution 
for you, please feel free to contact us again.

--
Brooke Rhead
UCSC Genome Bioinformatics Group


Klebig, Mitchell L. Ph.D. wrote:
> I would like to obtain a sequence conservation score, such as the
> percent identity scores obtained from BLAST analysis, for a given region
> of the human genome that is shown as having sequence conservation with
> another species in the browser.  If this can be done, please send me
> instructions on how to proceed.  (Note: I am not a bioinformaticist.)
> Thank you.
> _______________________________________________
> Genome maillist  -  Genome at soe.ucsc.edu
> http://www.soe.ucsc.edu/mailman/listinfo/genome