marylamb@milton.u.washington.edu (Mary Lamb) (10/12/90)
A colleague in the Philippines (a former graduate student in our lab) sent us the following question: Can you recommend a digitizing setup for analyzing RFLP data, something like the sequencing gel reader? (We have a gel reader and associated software from IBI. We have no connection with IBI, other than owning this equipment.) Does anybody know of such a setup for analyzing RFLP data? You can reply by posting to the net or to me by e-mail and I'll summarize if I get replies. Mary Lamb Department of Zoology NJ-15 University of Washington Seattle WA 98195 E-mail marylamb@u.washington.edu (I'm sorry about the previous message; I was in a hurry and forgot to remove the formatting from the word processor. Haste makes waste, my grandmother always said. :-)
marylamb@milton.u.washington.edu (Mary Lamb) (10/20/90)
[I had had a request from a colleague in the Philippines for recommendations about digitizing systems for RFLP analysis. I posted this request on the net and received information that I have forwarded to her. I don't have need for such a system at the present time, so I haven't pursued these leads any further. Here is a summary, and thanks to all of those who sent information. I have no connection with any of the products or companies mentioned. Mary Lamb, Dept. of Zoology NJ-15, University of Washington, Seattle WA 98195.] Summary: IntelliGenetics markets a video image acquisition system that is dedicated to acquiring, enhancing, reading and analyzing DNA sequencing film images to produce ASCII sequence files. They are now extending this system to allow it to function with restriction fragments and RFLP applications, and they expect that this new application will be available by the first quarter of 1991. Such a system would cost ~$28,000 including the cost of the computing hardware required (286 based MS-DOS system). (I have no connection with IntelliGenetics.) From DEUSTACHIO@MCCLB0.MED.NYU.EDU, I received the following interesting suggestion: "The FBI has constructed such a system, which they use for the analysis of their forensic human RFLP gels. My understanding is that is assembled from commercially available hardware and software, and in fact that one of their considerations in assembling the system was selection of cheap and readily available components (since they're hoping to export it to other police forensic labs). I do not have a list of the components and do not believe that such a list has been published. The person at the FBI Forensic Science Research and Training Center, Quantico VA 22135 responsible for the development of the system is Keith L. Monson, and he would be the person from whom to try to obtain more information. (If you decide to follow up on this, I'd be very interested in knowing the outcome.) A discussion of the FBI system in an FBI bulletin I have in front of me refers to a paper by Pun et al (Electrophoresis 6:268 (1985)) as the source at least of the basic strategy and perhaps of specific software and components as well. " [I did not get in touch with the FBI, but I did Xerox the paper and send to my colleague along with the message.] A couple of messages referred me to Native Plants, Inc. in Salt Lake City. They apparently use the same kind of IBI gel reader that we have in our lab for reading sequencing gels. (I have no connection with Native Plants, Inc. or IBI.) From: Francis_Ouellette@cc.sfu.ca I got a couple more leads: "...We have been looking into densitometers/scanners and a couple of the products we have looked at also do RFLP analysis. One of them is from Vision System Ltd, and they are based in Australia, (which is closer to the Philippines than we are :-) and they now have a rep in Vancouver. Their Australian address is: Second Ave Technology Park The Levels, South Australia 5095 Australia tel: (08) 349-5988 fax: (08) 349-5989 I have not seen their system yet (they are setting up a demo at UBC in a couple of weeks), but I have looked at a short video clip. . . . It seems like an adequate system. It has a large database manager of RFLP that comes with it, and the system modular, ie you can get the software/hardware you need to do what you need. For example you can also get the desk-top-publishing package to make figures from your captured data, or you could also get the densitometry software (which is different from the RFLP software). It appears to be a company geared toward forensic medicine, but it is trying to get into the scientific arena! I am not sure of the price range, but I think it is in the high 20K (if not low 30K) for a system with camera, light box, 386 computer and software The other system for which I did see a demo, was *very* impressive for its ability to do RFLP analysis. It has high resolution, very impressive software to detect and outline different band patterns and was of course also quite expensive! Also in the 30K range (but maybe high 30K), but here we are not talking PCs but a SUN Spark station! A very impressive machine! This is from BioImage, a software company that was recently (past year?) bought by Millipore. I am sorry I don't have the address here (now!) but I sure you have a millipore rep around there! The prices I mentioned are for here (in $US/$CAN ???) and are probably not too accurate, and may vary much (in either direction) for the Philippines. I hope the info is useful, and I know I don't need to say it, but I will anyway: I am not related, in any way, shape, or form to any of the companies above. I am just a grad student working away at his Phd and looking at things that my supervisor drops on my desk!"