BlockCounter.

Run BlockCounter

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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.
A second program by Dr. Mike Chapman, called Masker, is used to mask specified features of the global alignment. This script is also available and may be used to mask any named GFF file feature.

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