lane tracking

Bruce Roe BROE at aardvark.ucs.uoknor.edu
Thu Apr 11 10:01:55 EST 1996


Hi all,
	There recently have become two UNIX-based programs that are
alternatives to those available by ABI and ABI recently has announced
a patch for the most recent version of their Sequence Analysis program.

1. Getlanes - a UNIX based program to retrack the ABI gel.  This is
   an excellent little program which we find helpful, but requires
   that you transfer the "record.run" file (that's the big, 20 meg or
   so file containing all the raw data on the Mac) to a UNIX workstation.
   Here's the info:
	Genome Sequencing Center
	Washington University
	School of Medicine
	St. Louis, MO, USA

	URL: http://genome.wustl.edu/analysis/analysis.html
   Follow the link under:
	Four Color Electrophoretic Gel Image Analysis
     		Lane-Tracking - Lane Tracking Software
   to obtain a copy of this program.

2. Bass - a UNIX-based replacement for the ABI Sequence Analysis
	  Software.

  This is the first public release of Bass, the Unix port of Anthony
  Berno's Macintosh-based Sax program for tracking and processing
  automated sequencing gels.  Bass and its X-Windows front end, Grace,
  allows you to track, extract and base call ABI format sequencing gels
  without using any Macintosh-based sequence analysis software.

  The current release of Bass can be found at:

        http://www-genome.wi.mit.edu/ftp/pub/software/Bass/
        ftp://ftp-genome.wi.mit.edu/pub/software/Bass/

  The documentation and installation guide can be found in the file
  doc/BASS.html.

  In my opinion, this is a great beginning and Lincoln Stein at WI
  and Anthony Berno at Stanford should be commended for releasing
  this.  However, it took me several weeks of work to get all the
  programs (g++, Tcl, TK, and Netatalk) needed for Bass up an running
  on one of my SparcStations.  If you are not faint of heart and have
  a deep knowledge of UNIX, then the time spent is worth it.

3. Sequencing Analysis v2.1.2  March 1996 Update Patch

According to ABI readme file on their WWW site:
	http://www.perkin-elmer.com

  Sequencing Analysis 2.1.2 is a free update available to customers
  currently using version 2.1.1 Sequencing Analysis. If you have a
  previous version of Sequencing Analysis and would like to upgrade to
  version 2.1.1, please contact your Perkin Elmer representative. 
  Note the update files are only patches, or partial versions, of
  Sequencing Analysis. By installing the patch on a computer that
  currently contains Sequencing Analysis version 2.1.1, that copy of
  sequencing analysis is updated to version 2.1.2. This file will not
  install, except on computers that already contain version 2.1.1 of
  Sequencing Analysis.

I used fetch to connect to ABI's ftp site:    192.43.251.1
and just downloaded the patches from the directory:
	/pub/public/Sequencing/Sequence Analysis 2.1.2/373-377-310

ABI also has a program called "Edit View" which is in the directory:
	/pub/public/Sequencing
I've not yet installed either the patch or Edit View but did want
  to let everyone know of their availability.

Cheers to one and all......bruce
***************************************************************************
Bruce A. Roe, Ph.D    Department of Chemistry and Biochemistry
                      University of Oklahoma, Norman, OK 73019-0370, U.S.A.
Phone: (405) 325-4912 or 7610; FAX: (405) 325-7762; e-mail: broe at uoknor.edu
********************** http://dna1.chem.uoknor.edu/ ***********************

ps.  For those interested in the thread, here's the previous messages:

=> Ron,
=> 
=>    If your 377 gels have a consistant migration of the lanes then
=> something is definitely wrong.  The most likely cause of this would be a
=> heterogeneous gel.  To avoid this problem, I'ld make the following
=> recomendations
=> 
=>    1.  Use Long Ranger=81 gels.  They really do improve your results over m=
=> aking
=>          your own polyacrilamide mix.
=> 
=>    2.  Mix everything completely.  Too many people think that the gel will =
=> set
=>          if they don't pour seconds after adding the TEMED.  Mix a little l=
=> onger
=>          than you think is nescesary before pouring.
=> 
=>    3.  Look for patterns in the lane migration.  A consistant pattern might
=>          indicate an electrical problem (like a bum anode or cathode).
=> 
=>    Good luck, and make sure if you solve the problem to let everyone in
=> this group know how you did it.  These forums don't work if we don't share
=> answers as well as questions.
=> 
=> Eugen Buehler
=> buehler+ at pitt.edu
=> 
=> In article <4kfm5d$q5g at net.bio.net>, Ron Lundstrom <ron at eri.uchsc.edu> wrot=
=> e:
=> 
=> > Our lab is spending far too much time tracking lanes. We retrack more
=> > than half our gels. Hence they want me write lane tracking software,
=> > which I know won't be easy or short.
=> >=20
=> > ABI's lane tracking software does fine when the lanes run straight.
=> > In a previous job, I remember that some changes were made in the
=> > chemistry or gel preparation protocol that made things run straight.
=> > It wasn't 100%, but it helped a lot.
=> >=20
=> > Unfortunately, (`cause I'm the computer guy) I don't remember
=> > what was done. Can anybody give me some ideas on what to try?
=> >=20
=> > (We run ABI 377's with a 32 well comb.)
=> >=20
=> >      Thanks,
=> >      Ron L.
=> >=20
=> > --=20
=> > %*%*%*%*%*%*%*%*%*%*%*%*%*%*%*%*%*%*%*%*%*%*%*%*%*%*%*%*%*%*%*%*%*%
=> > *   RON LUNDSTROM              ron at eri.uchsc.edu                  *
=> > % Eleanor Roosevelt  1899 Gaylord Street   (303) 333-4515 (voice) %
=> > *     Institute      Denver, CO 80206-1210 (303) 333-8423 (fax)   *
=> > %*%*%*%*%*%*%*%*%*%*%*%*%*%*%*%*%*%*%*%*%*%*%*%*%*%*%*%*%*%*%*%*%*%
=> 





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