bb26+@andrew.cmu.edu (Brian Scott Butler) (04/05/91)
Since I'm not sure which bionet newsgroup to post this to I'll try this one. Recently, I came across some references to this. However, they were 1988 and 1987 and I was wondering whether anyone knew of more recent references. Also I was wonder if there was a general area that this topic falls into? (I'm trying to look into this and my searches are coming up blank....) Brian Butler bb26@andrew.cmu.edu
overt@antony (Christian Overton) (04/06/91)
In article <4byxW_200WB783NmhF@andrew.cmu.edu>, bb26+@andrew (Brian Scott Butler) writes: > >Since I'm not sure which bionet newsgroup to post this to I'll >try this one. > >Recently, I came across some references to this. However, they were 1988 and > 1987 and I was wondering whether anyone knew of more recent references. > >Also I was wonder if there was a general area that this topic falls into? >(I'm trying to look into this and my searches are coming up blank....) > >Brian Butler >bb26@andrew.cmu.edu Much of the work you refer to has been done by David Searls here at the Center for Advanced Information Technology, Unisys. Two references are: @INPROCEEDINGS{bio:searls88, AUTHOR = "David B. Searls", TITLE = "Representing Genetic Information with Formal Grammars", BOOKTITLE = "Proceedings of the Seventh National Conference on Artificial Intelligence, AAAI-88", ADDRESS = "San Mateo, CA", PUBLISHER = "Morgan Kauffman Publishers, Inc.", ORGANIZATION = "American Association for Artificial Intelligence", VOLUME = 2, PAGES = "386-391", YEAR = "1988", ANNOTE = " ADDRESS = 2929 Campus Drive, Suite 260 San Mateo, CA 94403"} @incollection(searls89a, Author="D.~B.~Searls", Title="Investigating the Linguistics of DNA with Definite Clause Grammars", Publisher="MIT Press", Year="1989", Booktitle="Logic Programming: Proceedings of the North American Conference, Vol. 1", Editor="E.~Lusk and R.~Overbeek", Pages="189--208", Annote="") He is also preparing a long chapter for a book edited by Larry Hunter (NLM). You might want to ask David for an advanced copy. His address is: =============================================================================== Dr. David B. Searls Center for Advanced Information Technology Unisys 70 East Swedesford Rd Paoli, PA 19301 (215) 648-2146 dbs@prc.unisys.com fax: (215) 648-2288 =============================================================================== Chris -- +-------------------------------------------------------------------------------+ | G. Christian Overton || Telephone: (215) 648-2420 | | Center for Advanced Information Technology || Internet: overt@prc.unisys.com | | Unisys || FAX: (215) 648-2288 |
holloway@bionette.cgrb.orst.edu (Jim Holloway - CS) (04/06/91)
Brian Butler asks: > Recently, I came across some references to this. However, they were 1988 and > 1987 and I was wondering whether anyone knew of more recent references. > > bb26@andrew.cmu.edu I assume that the 1987 and 1988 articles were by T. Head and D. B. Searls. There have been a couple of references to the paper by Tom Head. One of them is a paper in the International Journal of Computer Mathematics, volume 31, page 63 (1989) that I have not seen yet -- It may be useful. @string{bmb = "Bulletin of Mathematical Biology"} @article{Denninghoff1, author = "K. L. Denninghoff and R. W. Gatterdam", title = "On the undecidability of splicing systems", journal = "International Journal of Computer Mathematics", volume = 27, pages = "133--145", year = 1989, comment = "``In this paper the concept of a sequential splicing system is introduced. A sequential splicing system differs from a splicing system in that the latter allows arbitrarily many copies of any string in the initial set whereas the sequential splicing system may restrict the initial number of copies of some strings. The main result is that there exist sequential splicing systems with recursively unsolvable membership problem. The technique of the proof is to embed Truing machine computations in the languages.''"} @article{Head1, author = "T. Head", title = "Formal language theory and {DNA}: An analysis of the generative capacity of specific recombinant behaviors", journal = bmb, volume = 49, pages = "737--759", year = 1987, comment = "DNA is represented as a language over a four symbol alphabet. The actions of enzymes is represented as a set of operations on the strings over the four symbol alphabet. The closure of the original set of strings under the set of operations is analyzed using formal language theory. Two useful results are enumerating the possible DNA molecules that can be formed under specific conditions and secondly ``The relationships between or among the transforming activities made possible by different enzymes or combinations of enzymes may be made precise or at least conceptually clarified.''"} @inproceedings{Searls1, author = "D. B. Searls", title = "Representing Genetic Information with Formal Grammars", booktitle = "Proceedings of the AAAI 88", pages = "386--391", year = 1988, comment = "``This paper will first introduce the notion of applying general grammars to some simple DNA features, then discuss the linguistic power required for DNA, and then further elaborate a biological example along with an actual implementation and sample run.''"} --Jim