Software to read whole genomes?

Sean Eddy eddy at wol.wustl.edu
Mon Sep 29 18:03:36 EST 1997

In article <u97mbzbutj.fsf at wol.wustl.edu> eddy at wol.wustl.edu (Sean Eddy) writes:
  >  - the orientation of the read is annotated redundantly in parsable form
  >    in the DEFINITION field:
  >        zv37h04.s1 Soares ovary tumor NbHOT Homo sapiens clone 755863 3'
  >    i.e.:
  >        <clone plate location>.[s,r]1 <library> <clone ID> [5,3]' 
  >    where an s1 is a 5' read; r1 is a 3' read.

oops. The last line is correct; but the previous line is
wrong/misleading. The .r1 or .s1 indicates the direction of the read.
the 5' or 3' near the end of the line is followed by "similarity to
..." and indicates which strand a significant BLAST hit was seen on,
not which direction the sequencing was done in.


- Sean Eddy, Ph.D. 
- Dept. of Genetics, Washington University School of Medicine
- 660 S. Euclid Box 8232, St. Louis MO 63110, USA 
- mailto://eddy@genetics.wustl.edu http://genome.wustl.edu/eddy

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