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<a href="Bio-module.html">Package Bio</a> ::
<a href="Bio.NeuralNetwork-module.html">Package NeuralNetwork</a> ::
<a href="Bio.NeuralNetwork.Gene-module.html">Package Gene</a> ::
Module Schema
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<!-- ==================== MODULE DESCRIPTION ==================== -->
<h1 class="epydoc">Module Schema</h1><p class="nomargin-top"><span class="codelink"><a href="Bio.NeuralNetwork.Gene.Schema-pysrc.html">source code</a></span></p>
<p>Deal with Motifs or Signatures allowing ambiguity in the
sequences.</p>
<p>This class contains Schema which deal with Motifs and Signatures at a
higher level, by introducing `don't care` (ambiguity) symbols into the
sequences. For instance, you could combine the following Motifs:</p>
<p>'GATC', 'GATG', 'GATG', 'GATT'</p>
<p>as all falling under a schema like 'GAT*', where the star indicates a
character can be anything. This helps us condense a whole ton of motifs
or signatures.</p>
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<a href="Bio.NeuralNetwork.Gene.Schema.Schema-class.html" class="summary-name">Schema</a><br />
Deal with motifs that have ambiguity characters in it.
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<a href="Bio.NeuralNetwork.Gene.Schema.SchemaDNAAlphabet-class.html" class="summary-name">SchemaDNAAlphabet</a><br />
Alphabet of a simple Schema for DNA sequences.
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<span class="summary-type"> </span>
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<a href="Bio.NeuralNetwork.Gene.Schema.GeneticAlgorithmFinder-class.html" class="summary-name">GeneticAlgorithmFinder</a><br />
Find schemas using a genetic algorithm approach.
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<a href="Bio.NeuralNetwork.Gene.Schema.DifferentialSchemaFitness-class.html" class="summary-name">DifferentialSchemaFitness</a><br />
Calculate fitness for schemas that differentiate between sequences.
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<a href="Bio.NeuralNetwork.Gene.Schema.MostCountSchemaFitness-class.html" class="summary-name">MostCountSchemaFitness</a><br />
Calculate a fitness giving weight to schemas that match many times.
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<a href="Bio.NeuralNetwork.Gene.Schema.RandomMotifGenerator-class.html" class="summary-name">RandomMotifGenerator</a><br />
Generate a random motif within given parameters.
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<a href="Bio.NeuralNetwork.Gene.Schema.SimpleFinisher-class.html" class="summary-name">SimpleFinisher</a><br />
Determine when we are done evolving motifs.
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<a href="Bio.NeuralNetwork.Gene.Schema.SchemaFinder-class.html" class="summary-name">SchemaFinder</a><br />
Find schema in a set of sequences using a genetic algorithm
approach.
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<a href="Bio.NeuralNetwork.Gene.Schema.SchemaCoder-class.html" class="summary-name">SchemaCoder</a><br />
Convert a sequence into a representation of ambiguous motifs
(schemas).
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<a href="Bio.NeuralNetwork.Gene.Schema.SchemaFactory-class.html" class="summary-name">SchemaFactory</a><br />
Generate Schema from inputs of Motifs or Signatures.
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<td><span class="summary-sig"><a href="Bio.NeuralNetwork.Gene.Schema-module.html#matches_schema" class="summary-sig-name">matches_schema</a>(<span class="summary-sig-arg">pattern</span>,
<span class="summary-sig-arg">schema</span>,
<span class="summary-sig-arg">ambiguity_character</span>=<span class="summary-sig-default"><code class="variable-quote">'</code><code class="variable-string">*</code><code class="variable-quote">'</code></span>)</span><br />
Determine whether or not the given pattern matches the schema.</td>
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<a name="__package__"></a><span class="summary-name">__package__</span> = <code title="'Bio.NeuralNetwork.Gene'"><code class="variable-quote">'</code><code class="variable-string">Bio.NeuralNetwork.Gene</code><code class="variable-quote">'</code></code>
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<h3 class="epydoc"><span class="sig"><span class="sig-name">matches_schema</span>(<span class="sig-arg">pattern</span>,
<span class="sig-arg">schema</span>,
<span class="sig-arg">ambiguity_character</span>=<span class="sig-default"><code class="variable-quote">'</code><code class="variable-string">*</code><code class="variable-quote">'</code></span>)</span>
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><span class="codelink"><a href="Bio.NeuralNetwork.Gene.Schema-pysrc.html#matches_schema">source code</a></span>
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<p>Determine whether or not the given pattern matches the schema.</p>
<p>Arguments:</p>
<p>o pattern - A string representing the pattern we want to check for
matching. This pattern can contain ambiguity characters (which are
assumed to be the same as those in the schema).</p>
<p>o schema - A string schema with ambiguity characters.</p>
<p>o ambiguity_character - The character used for ambiguity in the
schema.</p>
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