want software, restrctn frag pattern ana

Farr, Tracy Farr at agresearch.cri.nz
Sun Nov 24 21:20:02 EST 1996

Can anyone suggest methods and software appropriate for analysis that might 
help us classify"supertypes" obtained from restriction enzyme analysis of 
Mycobacterium bovis (i.e. bacterial) DNA using three separate enzymes?

We are currently using Whole Band Analysis software from Bio Image on a Sun 
workstation to match samples on scanned gels to reference type patterns for 
each of three restriction enzymes. Types differ in the position of bands 
(from 22 to around 30 bands depending on enzyme), as well as their intensity 
and width, in some cases. So, bands are not just present or absent (1/0), 
but can also be higher, lower, narrower, broader, or of higher or lower 
intensity compared to any other particular reference type within the enzyme 
set of patterns. The Bio Image software can report matching results in 
dendrogram form (minimum, UPGMA, maximum, neighbour joining methods), and I 
am starting to investigate using this tool to generate a  classification, a 
measure of relatedness, for the types for each enzyme.

My question is this, though: what methodology might we use to go one step 
further, to infer/generate measures of similarity or clustering or 
relatedness between the "supertypes" we obtain for each sample by combining 
the types from each of the three enzymes?

We have recorded over 160 "supertypes", comprising the 70, 70 and 45 
different types recorded, respectively, for each of the three enzymes. Some 
of these supertypes differ from others by just one band difference in one of 
the three enzymes, while others show numerous pattern differences for all 
three enzymes.

While a novice in the field of molecular systematics, my preliminary reading 
has made me aware of the inherent problems in dealing with this sort of 
restriction fragment data as opposed to restriction site data. Still, we 
would like to generate some measure of relatedness for these supertypes.

I realise that some simplification of the data may be in order (reducing it 
to 1/0 for each possible band position, for instance).

Thanks in advance for any assistance or advice.

Tracy Farr

Wallaceville A.R.C.,
Upper Hutt,         Phone     64-04-528.6089
New Zealand         Fax  64-04-528.1380
Disclaimer: The above is a personal opinion and does not
reflect the official view of AgResearch Ltd.

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