[Genome] Processed pseudogenes

[Ann Zweig]

Hello Rebecca,

	The chain track includes all of the pseudogene mappings (whereas the 
net track keeps only the top alignment for each point in the genome). 
The chains include coherent alignments to paralogs, but the net discards 
then and keeps the ortholog.

	You can use the chainFilter program (available in our source code) to 
extract chains in a certain region from a chain file.  chainFilter has a 
lot of parameters so you can constrain the score (to get rid of the 
really short alignments).

	The Genome Browser and Blat software are free for academic, nonprofit, 
and personal use. A license is required for commercial use.

How to download the software: 
http://genome.cse.ucsc.edu/FAQ/FAQlicense#license3

You can obtain the source tree either via CVS:
	http://genome.ucsc.edu/admin/cvs.html
or a zip file:
	http://hgdownload.cse.ucsc.edu/admin/jksrc.zip

Please note the build instructions:
	http://genome.ucsc.edu/admin/jk-install.html

	All of the kent utilities output their usage message and command
line options by running them with no arguments.

	Download the chain file here: 
http://hgdownload.cse.ucsc.edu/goldenPath/ce4/vsCb3/



Regards,

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

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Rebecca Robilotto wrote:
> Hello,
> 
> I am working on a project that involves looking at the syntenic regions
> between C. elegans and C. Briggsae. In the chain and net files I found that
> it creates it own subset of syntenic regions. We have a set of pseudogenes
> that I want to compare with the syntenic regions to see if there is any
> relationship. I was reading the PNAS paper Evolution's cauldron:
> Duplication, deletion, and rearrangement in the mouse and human genomes and
> it mentioned that the NETFILTER program creates the syntenic subset and it
> includes the pseudogenes that arise from tandem duplication, but it
> eliminates the processed pseudogenes information. This paper discusses mouse
> and human, but I was wondering it has the same result with C. elegans and C.
> Briggsae. I would like to know about all the possible pseudogenes. Is there
> a way that I could get all the pseudogene information in the chain and net
> file and not just the duplicated ones?
> 
> Thank you,
> Rebecca Robilotto
> _______________________________________________
> Genome maillist  -  Genome at soe.ucsc.edu
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