making a "true" est consensus

Dr. Rob Miller rmiller at house.med.und.ac.za
Mon Dec 23 09:59:29 EST 1996


Hi there,
 
  Got some nucleotide sequence alignment/search/database questions for
you :
 
  How do we link 3' EST to 5' EST fragments from the same clone in order
 to make the linked consensus useful for subsequent searching, alignment
 and/or translation?
 
  We're developing a set of EST consensus sequences to submit to a
public
 database, and naturally we'd like these to be of the greatest utility
 possible.  We are thinking about the most useful format for the
submission.
 
  What is the  best way to link data for ESTs which come from the same
 clone -- a way that will preferably result in gaps inserted in the
linker
 region when someone comes along and searches the database with the
 sequence of the full clone ?
 
  Specifically, we'll be creating artificial consensus sequences from
two
 EST consensuses, e.g. a 5' EST AAAAAAAAAAAAAA and a 3' EST ZZZZZZZZZ.
 
  So our questions are:
 
   * What are the ramifications of
 
      using NNN's (unassigned) :
 
            AAAAAAAAAAAAAAAAAANNNNNNNZZZZZZZZZZZZZZZZZZ ???
 
      or using ----'s (gap) :
 
            AAAAAAAAAAAAA-----------------ZZZZZZZZZZZZZZZZ  ???
 
      between the two sequences ?
 
    * how many characters would be ideal ?
 
    * what else could be used ?
 
  We invite any helpful comments, and feel free to e-mail a copy of
 your reply to info at sanbi.ac.za to make certain we see it.
 
                                 thanks in advance,
 
                                                 rob.
 
 --

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 Robert T. Miller, Ph.D.                         
rmiller at house.med.und.ac.za
 
 Manager - Durban Satellite - South African National Bioinformatics
Institute
 
 Faculty of Medicine / Dept of Virology / University of Natal
 Private Bag 7 / Congella 4013 / Durban / South Africa
 phone +27 (031) 3603743                     fax +27 (031) 3603744 or
2604441

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