[Genome] Chain Vs Net tables

[Kayla Smith]

Hello Avi,

1.  Rather than list pros and cons, I can tell you where to find
information on these two types of tables.  Try this link:

http://genomewiki.ucsc.edu/index.php/Chains_Nets

And these links describe the chain and net file formats:

http://genome.ucsc.edu/goldenPath/help/chain.html
http://genome.ucsc.edu/goldenPath/help/net.html

Additionally, the details page of any chain or net track will have 
further information.

2.  The net table would be better for looking for orthologous regions in
other genomes.

3.  I recommend viewing these previously answered mailing list questions
because they talk about levels:
http://www.soe.ucsc.edu/pipermail/genome/2006-February/009869.html
http://www.soe.ucsc.edu/pipermail/genome/2006-August/011382.html

4.  See the answer to #3.  Level 1 corresponds to the top chain, while
level 2 means "gap".

I hope this information helps to get you started.  Please don't hesitate 
to contact us again if you require further assistance.

Kayla Smith
UCSC Genome Bioinformatics Group

On Tue, 20 May 2008, Fungazid wrote:

> Hello UCSC team,
>
> Thank you a lot for your help so far.
>
> As far as I understand chain tables represents all
> possible conserved regions of 2 given species. I saw
> that chain table tend to link specific target regions
> to many query regions (one to many).  For example:
> specific human target region is linked to 10 different
> regions in mouse genome. In order to reduce the
> enormous complexity of the chain representation, I
> thought of using net table.
> 1) But what are the pro and cons of each table (net Vs
> chain)?
> 2) Does net table better represents orthologous
> regions than chain?
> 3) About the levels (‘level’ column in MYSQL net*
> table): Are there overlaps between levels (for example
> level-1 position is chr1:100-200 and level-2 position
> is chr1:150-250)?
> 3) Why there are much less rows with level=1 than rows
> with level=2 (‘level’ column in MYSQL net* table)?
>
>
> Best wishes,
> thank you,
> Avi
>
>
>
>
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