wayner@svax.cs.cornell.edu (Peter Wayner) (10/04/88)
Does anyone have any references on software to do restriction mappings of DNA? Has anyone looked at the problem mathematically? Has anyone looked at the problem from the standpoint of a computer scientist? If anyone has any references, I would appreciate an answer. My two addresses are: wayner@svax.cs.cornell.edu wayner@crnlcs.bitnet Thank you. Peter Wayner
roy@phri.UUCP (Roy Smith) (10/04/88)
In article <21491@cornell.UUCP> wayner@cs.cornell.edu (Peter Wayner) writes: > Does anyone have any references on software to do restriction mappings of > DNA? Has anyone looked at the problem mathematically? Has anyone looked > at the problem from the standpoint of a computer scientist? Which problem are you talking about? Given the lengths of the fragments resulting from single and multiple digests construct a classical restriction map, or given a sequence find all the restriction sites in it? If it's the former, I can't help you much. If it's the latter, what you want to do is wait for the next issue of Computer Applications in the Biosciences in which I have a paper describing an algorithm for doing this in time proportional to the length of the sequence and independent of the number of restriction enzymes. To the best of my knowledge, it beats the pants of any other currently available algorithms. To be fair, Mount and Conrad (Nucleic Acids Research (1986) 14:443-454) make mention of a similar algorithm, but unfortunately do not describe the algorithm in any detail. -- Roy Smith, System Administrator Public Health Research Institute {allegra,philabs,cmcl2,rutgers}!phri!roy -or- phri!roy@uunet.uu.net "The connector is the network"
dd@beta.lanl.gov (Dan Davison) (10/04/88)
In article <21491@cornell.UUCP>, wayner@svax.cs.cornell.edu (Peter Wayner) writes: > Does anyone have any references on software to do restriction > mappings of DNA? At what level? Taking a restriction digest and assembling a unique map (if possible)? Prediction on what fragments will result from genomic cloning and sequencing? >Has anyone looked at the problem mathematically? Depends on your question. For assembly of restriction maps, there have been a few attempts to analyze mathematically; there were some papers by Mike Waterman in Nucleic Acids Research a few years ago. Mike and Eric (Erik?) Lander have an article in a issue of Genomics earlier this year on the subject. > Has anyone looked at the problem from the standpoint of a > computer scientist? Since the problem you are asking about is unclear, I can't answer this exactly. The answer is yes for both cases but to different degrees. > If anyone has any references, I would appreciate an > answer. > Peter Wayner Send me e-mail that goes to my office (dd@lanl.gov) and I will get them out. -- dan davison/theoretical biology/t-10 ms k710/los alamos national laboratory los alamos, nm 875545/dd@lanl.gov (arpa)/dd@lanl.uucp(new)/..cmcl2!lanl!dd "I think, therefore I am confused"