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Syntax is: splash InputFile [options]
Example:
running
splash histones.fasta
produces the file histones.fasta_0_209_0_3_8.txt
Description: This process the InputFile to extract all the
patterns that satisfy the discovery constraints set by the individual
command line options.
Input: InputFile must be the fully qualified path of a file
containing protein or DNA sequences in FASTA format.
Output: Discovered Patterns are
stored in in a file whose name, InputFile_A_B_C_D_E.txt, is determined
by the discovery parameters in the following way
| A |
This is the thread Id number. It is always 0, unless
the -t option is used. In that case, this value is used to
separate the results retuned by the individual processes |
| B |
It is the minimum support, in number of occurrences
or sequences, for this run. See options -j,
-%, and -u |
| C |
It is the minimum length of the pattern in tokens.
For instance, pattern A..BC.D.E has length 5. If C is 0, then the
minimum length is set by the value of k0 for the density
constraint. The latter is reported in the D value. See options -l,
-k, and -w |
| D |
It is the k0 of the density constraint.
See options -k and -w |
| E |
It is the w0 of the density constraint.
See options -k and -w |
Options: Several options are available. These control the
following aspects of the pattern discovery process:
Constraints
Statistical Constraints
Similarity Matrix
Parallel Execution
Format
Other |
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0. SPLASH
1. Algorithm
2. Performance
3. Pattern Discovery
Syntax
DNA/Protein Seq.
Constraints
Statistical Constr.
Similarity Matrix
Parallel Execution
Output Format
Other
4. Exhaustive Discovery
Syntax
5. Hierarchical Discovery
Syntax
6. Search
Syntax
7. References
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