Migration Distance on a Gel - (Oct/17/2010 )

This is probably a very silly question I have, but alas I don't know the answer so I must ask. Is the migration distance that one uses for Gel PCR a measure of length such as centimetres? I have a lovely picture of a gel I ran as well as standards that were both digested and not digested from HindIII and EcoRI, so I do have the data on the molecular weight of the fragments of my samples. I wish to plot these Fragment Size V. migration distance. So should I just measure the centimetres the fragments travelled on the X axis and place the fragment size on the Y axis? Thanks for any help on this question.

Cheers,
Murdock

That should be fine, though I would plot the distance on the Y axis and the size on the X.

I agree with bob in regards to the axis.

If you want to work out the exact band size of your unknown bands you can use an old program called SEQAID. Its an old MS-DOS based program from 1991 but it still works well! It calculates the length (in bp) of your unknowns. You just need to put in the size (bp)and mobility (i.e. length in cm) for each band in your ladder and then the mobility of your unknowns and it determines the band size. The output is very basic you could easily put the numbers into excel if you wanted a graph.

You can download it from here:
http://genamics.com/cgi-bin/genamics/software/db.cgi?db=software&uid=default&Classification=Sequence%20Alignment&view_records=Search&nh=6

Good luck!