> Sequence file for the evaluation set (Wasserman and Fickett, 1998)
    - fickett.data

> The evaluation matrices
    - fickett.mat

> JASPAR sample file
    - JASPAR_samples.matrices

    NOTE: The JASPAR matrices can be retrieved in whole from
    http://mordor.cgb.ki.se/cgi-bin/jaspar2005/jaspar_db.pl.

> MEME and MAST files:
    - meme_text_fickett_data_original_anr_15mtfs_8-12_6minsites_revcomp.txt
    - mast.meme_text_fickett_data_original_anr_15mtfs_8-12_6minsites_revcomp.txt.fickett.data.html
    - mast.meme_text_fickett_data_original_anr_15mtfs_8-12_6minsites_revcomp.txt.hg17_refseqs_14042006_unique.fa.html

> Motif comparison results from 'matrix_comparison.pl'
    - fickett_vs_fickett_matrices_60percent.out
    - fickett_vs_fickett_matrices_60percent_score.list
    - fickett_vs_fickett_matrices_60percent.tgz

    - fickett_vs_jaspar_matrices_60percent.out
    - fickett_vs_jaspar_matrices_60percent_score.list
    - fickett_vs_jaspar_matrices_60percent.tgz

> Conservation threshold trials
    - These files are available in the 'IC_variations_*' folders.

*******************************************************************************
Below is an example of how to run the programmes on this CD. This
example uses the data in Chapters 2 and 3.

./matrix_comparison.pl -m
meme_text_fickett_data_original_anr_15mtfs_8-12_6minsites_revcomp.txt -d JASPAR_samples.matrices -s stats.outout -c 60 -o fickett.output

For the permutation runs:

./matrix_comparison.pl -m
meme_text_fickett_data_original_anr_15mtfs_8-12_6minsites_revcomp.txt -d JASPAR_samples.matrices -s stats.outout -c 60 -p 100

Or using the fickett data:

./matrix_comparison.pl -m
meme_text_fickett_data_original_anr_15mtfs_8-12_6minsites_revcomp.txt -d fickett.mat -s stats.outout -c 60 -o fickett.output

For the permutation runs:

./matrix_comparison.pl -m
meme_text_fickett_data_original_anr_15mtfs_8-12_6minsites_revcomp.txt -d fickett.mat -s stats.outout -c 60 -p 100

The output file using the fickett data will be (showing the head of file):

################################################################################
                ############ Matrix comparison V1.0 ############
Input files:
## Motif file (e.g. MEME): meme_text_fickett_data_original_anr_15mtfs_8-12_6minsites_revcomp.txt
## Database file: fickett.mat
## Level of conservation: 60%
################################################################################
MOTIF_1 11
                  MA03                  Sp1 (11) 8.5151    [ 3 -> 11] - [ 1 ->  9]
                  MA01                MEF-2 (12) 0.7355    [ 1 -> 11] - [ 2 -> 12]
[...]

The permutation folders -- each folder representing one database
matrix length -- from the run are compressed together to a file
('permutations.tgz'). Decompress the tarball and run the second
programme ('permutations.pl'):

./permutation.pl -s stats.outout

This will produce a series of files, which represent the scores
and p-values for the best hit in each length category for each
motif. An output example is:

11/MOTIF_1      8.5151    97    0.97
12/MOTIF_1      0.7355     3    0.03

where the first field shows the length of the hit along with the
motif ID, here MOTIF_1. The second column is the dissimilarity
score for the match and the fourth and the fifth columns are the
frequency and p-value for the match.

This output can then be compared to the main result file
(fickett.output) for identification of the match.