What is BlockCounter?
BlockCounter analyses a FASTA formatted global alignment (e.g. the output of DIALIGN 2) or LAGAN for the presence of blocks of complete identity. The lengths of the blocks will lie within a user-defined range. The program generates data in the form of a frequency distribution (length of conserved block versus frequency of conservation) and (optionally) a plot of the positions of all specified block sizes in relation to a reference sequence.
For example, if the range of block sizes is between 10 and 20 nucleotides, the data generated might look like:
Block size Frequency 10 33 11 30 12 26 .. .. .. .. 20 7
The original BlockCounter script was designed by Dr. Mike Chapman.
Modifications were made by Dr. Ian Donaldson to create a plot of all the
block positions in relation to the reference sequence.