[Genome] the question of UCSC Genome Browser

[Rachel Harte]

Dear Lin Nai Song,

One way you can check this using the Genome Browser is to type in the
the gene name "ahrra" or "ahrrb" into the search/position box on the
Zebrafish danRer4 Browser. Then go to the Comparative Genomics section and
change the Human Net track to full for full visibility. The Net track
shows the best in genome alignment and so it is useful for finding
orthologs in other species. If you then click on the Human Net alignment
in the Browser image on one of the aligned blocks (not the gaps - lines
with arrows - in between) then you will see a details page. There you can
see a link that says "Open the Human Browser" at position corresponding to
the part of chain that is in this window. If you click on the link you
will see the Human Browser displaying the region that aligns to the part
of the chain that you saw on the Zebrafish Browser.

If you download either the axtNet files or the danRer4.hg18.net.gz, you
will find some differences between these alignments and those shown in the
Genome Browser web page. As we load the nets into our database, we filter
them with minGap=10. The downloads files contain the unfiltered net
alignments. For the net format, there are lines starting with the word
"fill" and these are the aligned blocks in the net. If the size of these
aligned blocks on the target side (that is danRer4 in this case, hg18 is
the query) are less than 10 then those aligned blocks are filtered out.
The net format is described here:
http://genome.ucsc.edu/goldenPath/help/net.html
The target size is the third field on the line starting with "fill".

I hope that this helps you. Please let us know if you have further questions.
If you find other differences between the web display and the axtNet
files, then please send us specific examples so that we can try to find
the problem.

Rachel

Rachel Harte
UCSC Genome Bioinformatics Group
http://genome.ucsc.edu


On Fri, 10 Nov 2006 M95360012 at ntou.edu.tw wrote:

>
> Dear Lady and Sir,
>                   I am user of UCSC Genome Browser. I want to check if the
zebrafish AHRRa (http://genome.ucsc.edu/cgi-bin/hgTracks?hgsid=80357424&clade=
vertebrate&org=Zebrafish&db=danRer4&position=ahrra&pix=620&hgsid=80357424&
hgt.dummyEnterButton.x=0&hgt.dummyEnterButton.y=0) and
AHRRb (http://genome.ucsc.edu/cgi-bin/hgTracks?hgsid=80357454&clade=
vertebrate&org=Zebrafish&db=danRer4&position=ahrrb&pix=620&Submit=submit&
hgsid=80357454) are conserved with human AHRR gene region
(http://genome.ucsc.edu/cgi-bin/hgTracks?position=chr5:357291-488224&hgsid=
80357482&knownGene=pack&hgFind.matches=NM_020731,). I download the
zebrafish-human  conserved region, but the result is not consistent with
what is shown at the web page. Is the web page’s algorithm for
comparative genomics different from the download file
(http://hgdownload.cse.ucsc.edu/goldenPath/danRer4/vsHg18/axtNet/
chr1.danRer4.hg18.net.axt.gz)?
>                                                                    Thanks a lot for you time,
>
>                                                                               Lin Nai Song,
>                                                                              Graduate Student .....
>         ......                                                                NTOU...
>
> _______________________________________________
> Genome maillist  -  Genome at soe.ucsc.edu
> http://www.soe.ucsc.edu/mailman/listinfo/genome
>