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repetititves sequences

Brian Fristensky frist at cc.umanitoba.ca
Mon Sep 12 17:06:06 EST 1994


In article BBE05D8A901FE00467 at vxircm.IRCM.UMontreal.CA, JOHANNE at IRCM.UMontreal.CA () writes:
> I am looking for a databases of repetitives sequences like Alu family
> from eukaryotes. I looked in the previous articles of Usenet group and 
> I found two alternatives:
deleted
> 2- make a small databank from Embl and Genbank with all the sequences
>    containing "repeat" in the definition. This can mix things...
> ___________________________________________________________________________
> Johanne Duhaime						tel (514)987-5556
> Institut de recherches cliniques de Montreal		fax (514)987-5644
> DuhaimJ at ircm.umontreal.ca
> ___________________________________________________________________________							
The FEATURES program from XYLEM can extract any features that are annotated
in GenBank entries. In your case, you might run the program, extracting
any features with feature keys such as

repeat_unit                {extracts just the repeat unit itself}
repeat_region              {extracts the entire region containing repeats}

Only parts of each sequence that are annotated as repeats will be extracted.
The XYLEM programs run under Unix and can be obtained by anonyous FTP to
directory 'psgendb' at ftp.cc.umanitoba.ca

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