|
| Option |
- z |
| Default |
not set |
| Description |
If set, the probability of discovering an equivalent
pattern in a random database with identical first order statistics
is computed and the corresponding ZScore is reported for each
discovered pattern. See Statistical Analysis Paper |
| Option |
- v |
| Default |
not set |
| Description |
if set, a list of locations where the
pattern occurs in the InputFile is reported. For each
pattern, the format is:
[id] [seqNo, No, TokenNo, ZScore] RegEx
TokOffId1, TokOffId2, TokOffIdTokenNo,
; [SeqId1, OffId1][SeqId2, OffId2]
... [SeqIdNo, OffIdNo]
| id |
sequential id of the pattern, starting at 0 |
| SeqNo |
Number of independent sequences that contain
the pattern |
| No |
Number of occurrences of the pattern |
| TokenNo |
Number of tokems in pattern |
| ZScore |
ZScore of pattern |
| RegEx |
String representation of the pattern as a
regular expression. |
| TokOffIdi
|
Offset, within the pattern, of the i-th token.
Tokens are numbered 1 to TokenNo. For instance, pattern
A..C.D would have offsets 0, 3, and 5 |
| SeqIdi |
Sequence Id, starting at 1, of the i-th
occurrence of the pattern |
| OffIdi |
Sequence Offset, starting at 0 of the i-th
occurrence of the pattern |
For an example of the file format, see the results
file for the sample histone I
database, obtained by running splash with default parameters and
the -v option
|
| Option |
-s[s|z|l|c] |
| Default |
not sorted |
| Description |
This option is used to sort the reported patterns
according to different criteria
| -sz |
Sort by (1) zscore (2) sequence support (3)
length |
| -ss |
sort by (1)sequence support, (2) zscore, (3)
length |
| -sc |
sort by (1) support (2) zscore (3) length |
| -sl |
sort by (1) length (2) zscore (3) support |
|
| Option |
-out filename (not implemented in this release) |
| Default |
Name is based on the input file and parameters |
| Description |
This allows to specify the name of the file where
the results will be reported |
|
|
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
|
