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Alu sequences within dbEST entries

Bob Obar 102063.2640 at CompuServe.COM
Wed Dec 18 07:50:36 EST 1996

  Several of the EST sequences I've been analyzing contain Alu 
sequences (specifically, the warning that shows up in the Definition
field is something like "similar to contains Alu repetitive 
element;contains element L1 repetitive element."

  Can anyone explain: 
  A) Why these sequences should be present AT AL in ESTs, which are 
supposed to represent cDNAs; or 
  B) What to do about them when aligning the ESTs and e.g. trying to
make contigs from them?  
  I'd like to just ignore them when analyzing the DNA they're fused 
to, but is this acceptable practice?  Is there any meaning in the 
presence of these sequences in some cDNAs but not others?
  Any help by email or posting would be greatly appreciated.

-- Bob Obar
102063.2640 at compuserve.com

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