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How to view overlapping sequences

Richard Durbin rd at sanger.ac.uk
Tue Nov 9 11:55:28 EST 1999


Hello Keith,

Aha, you ended up with AGR.  Congratulations.

It is not a sequence map that you need.  What glues separate clone
sequences together in the worm database is the *LINK* objects in the
Sequence class.  They have the separate entries as subsequences, e.g.

  Sequence : "LINK_Y39B6B"
  Source	 "SUPERLINK_CB_V"
  Subsequence	 "B0399" 556032 599668
  Subsequence	 "B0399.1" 568119 608616
  Subsequence	 "B0399.2" 558575 550832
  Subsequence	 "C14B4" 358654 346803
  Subsequence	 "C14B4.2" 347961 335484
  Subsequence	 "C25F9" 441189 397306
  Subsequence	 "C43D7" 346906 311926
  Subsequence	 "F21D9" 282729 244387
  Subsequence	 "F55C9" 312029 282626
  Subsequence	 "Y39B6B" 1 207022
  Subsequence	 "T26H2" 244487 206919
  Subsequence	 "Y43F8A" 358551 397406
  Subsequence	 "M04C3" 454554 441086
  Subsequence	 "Y43F8B" 454454 556132
  Subsequence	 "Y43F8C" 599568 720059
  Subsequence	 "Y116F11A" 719951 733832
  Subsequence	 "M04C3.1" 446349 440693

We use the Overlap_right and Overlap_left tags in acedb to store the
overlap information, then use a script as in the next message to
rebuild the link objects, which are what acedb needs.

Richard
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