suggestions for restrctn frag data treat

Farr, Tracy Farr at agresearch.cri.nz
Sun Dec 1 21:07:19 EST 1996


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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.


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Tracy Farr

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