[Genome] Question about UCSC genome browser.

[Ann Zweig]

Hello Wei,

	If you have sequences, you can BLAT those against the latest human 
genome assembly.  BLAT on DNA is designed to quickly find sequences of 
95% and greater similarity of length 25 bases or more. It may miss more 
divergent or shorter sequence alignments. It will find perfect sequence 
matches of 33 bases, and sometimes find them down to 20 bases. BLAT on 
proteins finds sequences of 80% and greater similarity of length 20 
amino acids or more.

	BLAT will return all of the hits in the genome including %identity.  To 
read more about using the BLAT tool, see this help page: 
http://genome.ucsc.edu/goldenPath/help/hgTracksHelp.html#BLATAlign

	If you make a custom track out of your BLAT results, you will
be able to view your sequence hits in conjunction with any other track 
in the genome browser, such as the SNP track.  To read more about 
creating Custom Tracks, see this help page: 
http://genome.ucsc.edu/goldenPath/help/hgTracksHelp.html#CustomTracks

	This should be enough to get you started.  Please feel free to write 
back to the list if you need more detailed instructions.

Regards,

----------
Ann Zweig
UCSC Genome Bioinformatics Group
http://genome.ucsc.edu



	
Wei Guo wrote:
> To whom it may concern,
> 
>  
> 
> Can custom sequences such as many short Solexa reads or longer consensus
> gene sequences, be uploaded to UCSC genome browser, be aligned to the
> human genome and be shown with regions of known and novel SNPs, indels,
> if any? Or can the genome browser show align percent, coverage depth,
> etc of uploaded custom sequences?
> 
>  
> 
> Best regards,
> 
> Wei 
> 
>  
> 
> Wei Guo, PhD
> 
> Bioinformatics Scientist
> 
> Ambry Genetics  
> 
>  
> 
> 100 Columbia, #200
> 
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