Path: utzoo!attcan!uunet!clyde.concordia.ca!ccu.umanitoba.ca!frist
From: frist@ccu.umanitoba.ca
Newsgroups: bionet.general
Subject: Re: 'Face' representations of nucleic acid sequences
Message-ID: <1990Sep6.151026.23046@ccu.umanitoba.ca>
Date: 6 Sep 90 15:10:26 GMT
Organization: University of Manitoba, Winnipeg, Canada
Lines: 58


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
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