**** MOFEXT v1.0.3 ****

MOtiF search and EXTraction tool. The program finds short sequence motifs in a motif database.

Usage: mofext -d mypatterns1.list mypatterns2.list -q GGATCC TTGANTGA -m matrix -w 10 -c 0.95

Options:
~~~~~~~~
-h     Display full help.
-d     Databases to search. Space separated, maximum 50.
-q     Query patterns. Space separated, maximum 50.
-m     The similarity matrix.
-w     Wordsize. Default: 6.
-c     The similarity percentage limit (cutoff). Default: 0.8.
-o     Output format. See below.

Example:

mofext -d mypatterns1.list mypatterns2.list -q GGATCC TTGANTGA -m matrix -w 4 -c 0.5

Matrix:
~~~~~~~
 The matrix used by mofext is a plain text file. Each row ends with a newline character.
 Columns are separated by one or more spaces. The matrix is quadratic, so A[j,i] = A[i,j].
 The number in the upper left corner denotes the matrix size. See default matrix included
 in the source.

Motif list:
~~~~~~~~~~~
 The motif list file used by mofext is a plain text file. Each row ends with a newline character.
 The motif list file must have at least 2 columns, separated by spaces or tabs. The first column
 is a UNIQUE motif id. It can contain any characters except space, newline or tab. The second
 column is the sequence (pattern) of the motif. The available characters are the ones defined in
 the matrix file. Additional columns are ignored by the program.

Output:
~~~~~~~
 The -o option sets the output format of the program. The following characters represent an output
 element. The default is ieqd.
 i: ID column.
 s: Score.
 e: Extended score.
 p: Probability value.
 d: Hit subsequence.
 D: Full hit sequence.
 q: Query subsequence.
 Q: Full query sequence.
 F: The position of the first base of the hit subsequence in the full hit sequence.
 f: The position of the first base of the query subsequence in the full query sequence.
 %: The similarity percent score of the hit/query subsequence pair.
 Example: mofext -d mypatterns1.list -q GGATCC -m matrix -o ied
 The program prints out the ID, extended score and the hit subsequence.