INCHWORM calculates the sizes of molecules based on their electrophoretic mobility relative to a set of standards. Although the program was developed for the analysis of DNA in borate-containing buffers (TBE, TAE) it should work equally well for any molecule having an evenly- distributed charge-per-unit-length such as denatured proteins in SDS-glycine buffers. The nature of the matrix (agar, agarose, polyacrylamide, paper, etc) should have little effect on calculations unless gradients are employed.
The program was written in Perl for use on the WEB. Calculations are based on the theory that under the influence of an electric field a molecule will migrate with a velocity inversely proportional to the logarithm of its mass. In practice, mobility only approximates the theoretical relationship. (This fact can be seen in the gradually increasing slopes of the standards). However, the use of appropriate standards can minimize errors due to this discrepancy.
The user is reminded that calculations can be no better than the measurements on which they are based and, ultimately, on the quality of the electrophoretic separation. Calculations for molecules outside the size range of the standards should be considered only rough approximations. (They are based on the slope between the nearest pair of standards.)
