Training

In this mode SPLASHSearch can be used to precompile a PSSM model so that it can later be used in a multi-model search. For instance, the file  model.fa_0.motifs, obtained by running splash with the -f metaSPLASH option on the training set model.fa, can be compiled into its corresponding binary model file, model.fa_0.motifs.bin, by running:

splashsearch -build 
             -model model.fa_0.motifs 
             -train model.fa
             -seqs  database

where database is a database with at least 100 sequences and a residue distribution that approximates the average distribution of the sequences against which the search will be performed. For instance, this could be a subset of the SWISSPROT database.

The complete syntax is provided in the Search Syntax document.

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