From owner-cellbiol@net.bio.net Thu Dec 26 22:00:00 1996
Path: biosci!rutgers!cnn.Princeton.EDU!cbgw1.lucent.com!cbgw3.lucent.com!news.pbi.net!news.bbnplanet.com!su-news-hub1.bbnplanet.com!news.sgi.com!newsfeed.internetmci.com!compuserve.com!news.production.compuserve.com!news
From: Bob Obar <102063.2640@CompuServe.COM>
Newsgroups: bionet.cellbiol,bionet.molbio.evolution,bionet.molbio.gdb,bionet.molbio.genbank,bionet.molbio.proteins
Subject: Alu sequences within dbEST entries
Date: 18 Dec 1996 12:50:36 GMT
Organization: Matritech, Inc.
Lines: 17
Message-ID: <598pas$1s2$1@mhafc.production.compuserve.com>
Xref: biosci bionet.cellbiol:6312 bionet.molbio.evolution:5458 bionet.molbio.gdb:555 bionet.molbio.genbank:2460 bionet.molbio.proteins:9631

  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@compuserve.com

.