ALSE - An Introduction

1. Command Line Version of ALSE
   • Downloading and Compiling the source code
   • Running ALSE
2. Web Version of ALSE
3. FASTA sequence data Format
4. Output Format

ALSE is written in C++, it can be compiled with the GCC C++ compiler version 3.00 or above. You can get the source code from the ALSE webpage. The file is in the format ALSE_v????.tar.gz where v???? is the version number.
Unix prompt is shown as "$". Un-tar the file and compile the ALSE by doing:

$ tar zxvf ALSE_v???.tar.gz
$ cd ALSE
$ make clean
$ make

SYNOPSIS

    ./find_motif [OPTIONS] -t <true seq file> -f <false seq file>

where

1.  <true seq file> is the full path name of the sequence file that is known to contain the motif(s). It is in the FASTA format.
2.  <false seq file> - sequence data file that consist of the background sequences, also in FASTA format.
3.  [OPTIONS] fields specify the parameters used for running ALSE. They can be any of the following, appeared in any order. When a particular option is not set or not specified in the command line, the default value is used in ALSE.
   

        -m, --motif

              Length of the motif to be discovered

              (default 6)

   
        -r, --no_reverse

              do not test the reversed sequence

   
        -O, --output

              output HTML filename

              (default ./output.html)

   
        -b, --binding

              Specify the maximum number of motifs in a sequence

              (default 2)

   
        -s, --seeds

              number of seeds used for s tuning iteration

              (default 100)

   
        -h, --help

              Disply the command and options information

[FASTA] := [SEQUENCES]

[SEQUENCES] := [SEQUENCE]
               [SEQUENCES]

[SEQUENCE] := >[SEQUENCE-NAME]
              [SEQUENCE-DATA]

[SEQUENCE-DATA] := [DNA_CHARACTER] [SEQUENCE-DATA]

[SEQUENCE-NAME] := A|B|...|Z | a|b|...|z | 0|1|...|9 | _ | - 

[DNA_CHARACTER] := A|C|G|T

1. Program parameters
   Here shows information and of the input data, including the options issued and the names pf input sequences and total execution time.
   
   
2. List of motifs
   Here outputs a list of the found motifs in order of the p-values. Each motif's p-value and alpha are also displayed
   e.g.
   
   
3. Detail for each motif
   e.g.