SB06@liverpool.ac.uk ("Dr. R.J. Beynon") (09/03/90)
Sometime ago I recall an article on representation of nucleic acid structures using something similar to Chernov (?) representations of multivariate data using face cartoons. The idea seems daft, but objective tests have proven that humans are particularly good at associating facial expressions, and of, for example, identifying 'strangers' in a data set. Can anyone help me with a reference to the original article, or better still, to a program that embodies some of these principles? If anyone knows of any other 'bizarre' methods of representing sequences, I'd like to know about them (I already know about CGR, PUPPY and an A4 page full of A's, G's, T's and C's :-> ) Thanks in advance, Rob Beynon ============================================================================== ! Rob Beynon ! PHONE: (051) 794 4359 ! ! DEPARTMENT OF BIOCHEMISTRY ! FAX: (051) 794 4349 ! ! UNIVERSITY OF LIVERPOOL ! JANET: SB06@UK.AC.LIV.IBM ! ! PO BOX 147 ! ! ! LIVERPOOL L69 3BX ! ! ! UNITED KINGDOM ! ! ==============================================================================
NUM255@NRCCAD.NRC.CA (09/04/90)
The only one I can recall is the method published by Cowin, Jellis and Rickwood in NAR 14 : 509-515, 1986. But I think I also saw a reference (in Biotech News perhaps?) to a system deviced by some Japanese group in which the nucleotides were represented as musical notes. The ability of the human year to identify tunes was being proposed as a way to detect specific nucleotide motifs... Have fun...! By the way, I think that we met a couple of years ago in Cambridge, am I right? -Jose- J. Campione-Piccardo Natl. Lab. Mol. Oncol. Ottawa, Ontario CANAN Ottawa, Ontario CANADA
AKC01@IBMVM.RRZ.UNI-KOELN.DE (Kay Hofmann) (09/04/90)
regarding unusual DNA representations: Do you already know HYLAS (E.Hamori et al. CABIOS 4:263-269, 1989) representing the sequence as a 3-dimensional curve in space? *-------------------------------------------------------------------* Kay Oliver Hofmann Institut fuer Biochemie (med. Fakultaet) INTERNET Universitaet Koeln akc01@aix370.rrz.Uni-Koeln.DE Joseph Stelzmann Str. 52 D-5000 Koeln 41 (West Germany) BITNET: Tel. +49 (221)4786980 akc01@dk0rrzk1 *-------------------------------------------------------------------*
rec@arris.com (Roger Critchlow) (09/05/90)
And there's: Clifford A. Pickover, DNA vectorgrams: Representation of cancer genes as movements on a 2D cellular lattice. IBM J. Res. Develop, 31:1, Jan 1987, 111-119. also described in his recently published book. Would you post a summary of the responses? A daft representation biblio- graphy? -- rec --
frist@ccu.umanitoba.ca (09/06/90)
Summary: Example of 'bizzare' method of representing sequences Expires: References: <9009031724.AA16629@genbank.bio.net> Sender: Brian Fristensky Distribution: Organization: University of Manitoba, Winnipeg, Canada Keywords: sequence representation In article <9009031724.AA16629@genbank.bio.net> SB06@liverpool.ac.uk ("Dr. R.J. Beynon") writes: >Sometime ago I recall an article on representation of nucleic acid structures >using something similar to Chernov (?) representations of multivariate data >using face cartoons. stuff deleted >If anyone knows of any other 'bizarre' methods of representing sequences, I'd >like to know about them (I already know about CGR, PUPPY and an A4 page full >of A's, G's, T's and C's :-> ) >============================================================================== >! Rob Beynon ! PHONE: (051) 794 4359 ! >! DEPARTMENT OF BIOCHEMISTRY ! FAX: (051) 794 4349 ! >! UNIVERSITY OF LIVERPOOL ! JANET: SB06@UK.AC.LIV.IBM ! >! PO BOX 147 ! ! >! LIVERPOOL L69 3BX ! ! >! UNITED KINGDOM ! ! >============================================================================== Sounds a bit too much like the face on Mars to me. :-) But I guess that proves the point about the ability of people to recognize faces in the midst of visual 'noise'. Anyway, to answer your question, one example of 'bizarre' methods of representing sequences is stave projection, as set forth in the following article: Cowin, JE, Jellis, CH and Rickwood, D (1986) A new method of representing DNA sequences which combines ease of visual analysis with machine readability. Nucl. Acids. Res. 14: 509-515. Briefly, stave projection uses a musical staff as a framework for displaying sequences. If you think of a sequence being written below a treble staff, then a dot (quarter note without the stem?) is placed within the staff for each nucleotide. Going up the scale, cytosine is represented by the note F, thymine by A, adenine by (middle) C, and guanine by E. Although this sounds funny, it really is quite striking how easy it is for the human eye to pick out repeats and familiar patterns when sequences are represented in this fashion. However, I have not seen this approach used in the literature, other than in this article. =============================================================================== Brian Fristensky frist@ccu.umanitoba.ca Assistant Professor Dept. of Plant Science University of Manitoba Winnipeg, MB R3T 2N2 CANADA Office phone: 204-474-6085 FAX: 204-275-5128 ===============================================================================