[Genome] Help

[Rachel Harte]

Hello Wen-Xin,

In this region, even though there is some conservation at the right of the
region, it is very low apart from one small region which shows some
conservation (chr10:52,141,457-52,141,489). That is partly because the
similarity between the genome sequences aligned to this region is not high
and also, because, for many of the species there is no sequence aligning to
this region of the human genome. This may mean either that there really is
no sequence in those genomes that can align well to this region or that the
region in those genomes that should align has just not been sequenced yet
because the genome assemblies for those species are still being sequenced
and are not yet finished. You can choose to see all the species used to
create the conservation track by first clicking on the blue or gray bar to
the left of the track in the Browser image. You can then select more species
in the "Pairwise alignments" section. If you scroll down this page, you will
also see a description of the conservation track which explains how it was
created together with relevant publications.

The regions from each species' genome that are shown to align to this
region of the human genome are chosen because they are the best aligning
region of each species' genome to the human genome. For each species, the
pairwise Blastz alignments for that species' genome to the human genome
are created and the best in genome alignment is selected (as for the net
tracks for each species). Then a program called Multiz is used to create
the multiple alignment from these pairwise alignments. For further
details, see the Blastz, Chain/Net, Multiz and PhastCons publications as
shown on the track description page.

If there is obvious conservation then this indicates homology between
the genome sequences in the multiple alignment. The higher the
conservation then the greater this homology. This indicates that this
region is likely to have an important function and so it has been
conserved throughout evolution e.g. exons of a gene, gene regulatory
regions etc. For example, if you look at the region,
chr7:127,680,921-127,682,736, you can see that there is a large peak of
conservation that coincides with an exon of the leptin (LEP) gene in the
UCSC Gene and RefSeq Genes tracks. This is a protein-coding region that is
highly conserved in many species throughout evolution. Notice that at the
edges of the 5' end of the exon (at the exon/intron boundary), the
conservation drops off very sharply (it quickly becomes very low) in the
intron where the genome sequence does not code for protein.

I hope that this helps you. Please let us know if you have further questions.

Rachel

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


On Thu, 17 May 2007, ZhengWenXin wrote:

>
> Dear Prof.
>        Thank you for your detailed guidance. I¡¯m more familiar with the Genome Browser.
>        Would you please give me some further discussion about the biological meanings of the conservation track? I queried the sequence from 52,140,973 bp to 52,141,573 bp on chromosome 10 of the human genome (hg18) through the Genome Browser. It shows that the conservation is obvious at the right of the locus (about 52,141,260 bp). Firstly, I wonder if it means that the biological characters such as homology or some other characters are obviously different on the two sides of the locus (about 52,141,260 bp). Secondly, following the guidance, I found that the sequence of mouse which is used to be aligned against the human sequence (from 52,140,973 bp to 52,141,573 bp on chromosome 10) is on chromosome 10 of the mouse genome. But that of the rat is on chromosome 20. Would you please tell me how to decide which sequence should be chosen to align with the objective sequences? And if the conservation is obvious, does it mean the objective sequence has some special correlations wi
>  th those genomes, such as homology?
> Thanks a lot for your patience. I am looking forward to hearing from you. Your help to my study would be greatly appreciated.
>
> Best wishes,
>
> Wen-Xin
>
> Wen-Xin Zheng, PhD candidate
> Bioinformatics Center
> Tianjin University
> Tianjin 300072
> China
> Fax: +86-22-27402697
> Website: http://tubic.tju.edu.cn
>
>
>
>
>
>
>
>
>
> Wen-Xin:You can find out what else is going on in your region of interest,chr10:52,140,973-52,141,573 by turning on other annotation tracks, suchas the UCSC Genes track or the RefSeq Genes track.  I don't see anygenes aligning there for those two tracks, but you can try looking atother tracks.If you click on the conservation graph itself, you're taken to a detailspage.  On this page you'll see a blue "B" an "D" next to the names ofthe aligning assemblies.  The "B" link will take you to the relevantposition in the other assembly while the "D" link will give you DNA.For example, clicking on the "B" link next to the "mouse" assembly takesyou to the mm8 browser at this position: chr10:73,249,778-73,250,024.I hope this information is useful to you.  Please don't hesitate tocontact us again if you require further assistance.Kayla SmithUCSC Genome Bioinformatics GroupZhengWenXin wrote:>  >  > Dear Prof. Archana,>  >        Thank you for your kindly responds. >        I still have tw
>  o questions, after reading the description. I queried about the sequence from 52,140,973 bp to 52,141,573 bp on chromosome 10 of the human genome (hg18) through the Genome Browser. I¡¯m not sure if this sequence contains a gene or some other elements. >        The second question is that the result of the conservation track has an obvious turning point in the middle part (about 52,141,260 bp). I wonder if this turning point has some special meanings. Furthermore, would you please tell me which parts of the sequences of the other species are used to be aligned against the sequence from 52,140,973 bp to 52,141,573 bp on chromosome 10 of the human genome (hg18)? For example, which sequence in the mouse genome is used to be aligned against the human genome in the conservation track? Is this sequence a gene or some other elements?>        Thanks again. I am looking forward to hearing from you. Your help to my study would be great appreciated.>  > Best wishes,>  > Wen-Xin>  > Wen-
>  Xin Zheng, PhD candidate> Bioinformatics Center> Tianjin University> Tianjin 300072> China> Fax: +86-22-27402697> Website: http://tubic.tju.edu.cn>
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