Gel Patterns

Danielle et Jean Thierry-Mieg mieg at kaa.crbm.cnrs-mop.fr
Fri Apr 8 06:55:19 EST 1994


In january i wrote a new display for finger print analysis
adapted for the nematode
then i reused it for the genethon data
now i realise that it could be used more widely for any pattern

1) Present system

The nematode ?Clone has a tag somewhere that syas
  FingerPrint UNIQUE Float REPEAT

then in the pmap display i hooked a boxmenu on the clones that says
fingerprint

to invoke the fingerprint display, uou pick the menu in a displayed clone
this starts the FP-display
then you can import other clones like in GridDisp or KeySetAdd/Remove
or import a whole keyset

there is always a single active FP-display that coaligns all the patterns
the lines in this pseudogel can be switched easilly, 
the common lines can be highlighted
details on the object obtained by single and double clicks
it zooms etc correctly

1.2) Difficulty
the way to invoke the system is from pmap display only
it can t be used in some other class

2) Genethon dta
those are a bit more general
what Cohen and co did is to cut yacs by several restriction enzymes
then lightup those bands hybridizing to a repeated sequence THE

so i have then a model

?Yac FingerPrint ?Probe ?Motif UNIQUE Float REPEAT

Probe is THE or another one,  Motif is the restriction enzyme used

3) A possible generalisation is to attach the FingerPrint display
to nay object that will have the Fingerprint tag
all of these could then be imported

certainly the magic construct should be 

  FingerPrint #FingerPrint

nevertheless: How do we popup the FP-display to start with, from main menu ?

how do we document this extra magic tag ?

a possibility is to have a FP class, but i am rather against that

*************************************
here is the proposal by Sam:


I think we need a very general solution for band
patterns, one that we can use to represent any
banding pattern whether or not restriction enzymes
are involved or if a locus is known--for example
protein gels

the minimum needed I believe is:

a way to identify a lane
a way to identify every band in the lane
a way to give every band a size

I could then use this to build more complicated things,
e.g. to represent the plant genome database conception
of "?Gel_Pattern".

suppose this thing was called #Lane

maybe it looks like this

?Lane Lane Text Text UNIQUE Float

first  Text is lane designation
second Text is band designation
third  Float is band size

so I could have

Lane A Band1 12.5
Lane A Band2  9.3
Lane A Band3  4.2
Lane B Band1  9.7
Lane B Band2  0.8

etc

in my higher level object I could annotate each lane as desired
and associate it with enzymes, loci, etc?

now how to display this? You would display only if you
were looking at an object that had #Lane(s)?

Sam

********* end of Sam's ***********************

i dont really like that because in cases i know
there are plenty of lines that nobody wants to name

so FingerPrint Line Float
               MappedLine Text Float
               DoublyMappedLine Text Text Float

is more economic, but is also very silly
remeber that genethon data is several millions floats
so silly tags are expansive

*******

Feedback hoped for,
Jean




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