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) *
=> > %*%*%*%*%*%*%*%*%*%*%*%*%*%*%*%*%*%*%*%*%*%*%*%*%*%*%*%*%*%*%*%*%*%
=>
