[Genome] human 3' utr seqs that do not cross hyb to orthologous rat gene seqs

[Ann Zweig]

Hello Richard,

	Yes, you can do this using tools available on the UCSC Browser website. 
  The general steps will include getting the 3' UTR positions you are 
interested in, using the liftOver tool to lift those positions to the 
rat genome, getting the sequence for both human and rat, then running an 
aligner on the two sequences.

	You can get the 3' UTR positions for your genes of interest by using 
the Table Browser tool on our website ('Tables' from the top blue 
navigation bar).  Choose your gene set (e.g. RefSeq or UCSC Known 
Genes), then enter your gene names in the "identifiers 
(names/accessions)" field.  Choose BED as your output format.  This will 
give you positional information for the 3' UTRs of all of your genes in 
human.

	To convert these positions to rat, use the liftOver tool: 
http://genome.ucsc.edu/cgi-bin/hgLiftOver

	Get the underlying sequence for both human and rat by creating a custom 
track, then choosing that custom track in the Table Browser to get the 
sequence.  See this FAQ for more details on this step: 
http://genome.ucsc.edu/FAQ/FAQdownloads#download32.

	Once you have the sequence for both human and rat, use an alignment 
tool to align the sequence and filter on percent similarity.

	This should be enough to get you started.  If you need more detailed 
instruction, don't hesitate to write back to the list.


Regards,

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

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Richard Dixon wrote:
> Dear Genome people,
> 
>  
> 
> Please could someone tell me if it is possible to use the UCSC browser
> to solve my task.
> 
>  
> 
> I have a list of ~1500 human genes for which I want to find the 3'utr
> seqs (~70-100bps) that are NOT similar (eg :<75% similar) to the
> orthologous Rat gene seq.
> 
>  
> 
> This is to design human oligo probes that will not cross hyb with rat
> genes.
> 
>  
> 
> I would really appreciate your advice on this
> 
>  
> 
> Rick
> 
>  
> 
> Dr. Richard Dixon
> 
>  
> 
> Medical Solutions plc
> 
> 1 Orchard Place
> 
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> 
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> 
> United Kingdom
> 
>  
> 
> Phone: +44 (0)115 973 9027
> 
> Email: richard.dixon at medical-solutions.co.uk
> 
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> 
> Fax: +44 (0)115 973 9021
> 
>  
> 
> 
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