[Genome] mRNA\genome side by side alignment

[Brooke Rhead]

Hello Shahar,

We do not keep the side-by-side alignments in files.  The alignment 
displays  in the Genome Browser are generated on the fly from the psl 
table associated with the RefSeq Genes track, called 'refSeqAli'.  (psl 
format is described here: http://genome.ucsc.edu/FAQ/FAQformat#format2)

There is not a way to generate these alignment displays via the Table 
Browser.  However, we do have a utility in our source tree called 
'pslPretty' that can generate the alignment displays from a psl and the 
corresponding sequence files.  Information about downloading the Genome 
Browser source (which is free for academic, noncommercial, and personal 
use) is located here:

http://hgdownload.cse.ucsc.edu/downloads.html#source_downloads

Once the source is installed and the utilities made, you can run the 
'pslPretty' command without any arguments to get a usage statement.

The zebrafish sequence files are available for download here, as well as 
the zebrafish refSeq mRNA sequences:

http://hgdownload.cse.ucsc.edu/goldenPath/danRer4/bigZips/

I hope this information helps.  If you have any further questions, pleas 
do not hesitate to write back to this list.

--
Brooke Rhead
UCSC Genome Bioinformatics Group


shahar alon wrote:
> I'm trying to find mRNA\genome side by side alignment for all the RefSeq
> genes in the zebrafish.
>
> Is there a file with that data on your servers?  
>
> (The file should contain the actual alignment of the mRNA to the genome and
> not the statistics of the alignment)
>
> If there isn't such a file, how can I create one using the Table browser?
>
> Thank's
>
> Shahar alon, Israel 
>
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