SiteFinder

Data Stream Processing > Processing Modules > General manipulation Modules

Description

The SiteFinder processing module performs basic genomic sequence identification using either IUPAC or Motif patterns. This module is a feature emitter which scans the genomic sequence for motif site patterns. Algorithm is based on PWM matric and the MATCH scoring method, but can be configured to search for string literals, IUPAC strings or PWM motifs. General purpose site searching tool which can be configured for everything from:

• restriction sites
• Cas9 sites
• Transcription-factor binding sites

Parameters

• <strand> : specify which genomic strand to search: +: positive strand only, - reverse strand only, or = search both strands
• <mismatches> : mismatches allowed. default is 0 for perfect match.
• <score_cutoff> : 0-1 score cutoff value for matches. Default is 1.0 for perfect match.
• <site_name> : the name given to each generated feature. for example "EcoR1"
• <iupac_seq> : specify the search pattern using IUPAC sequence
• <pwm> : specify the search pattern using PWM motif matrix format.

Example

Here is an example using SiteFinder to find all Cas9 sites

<zenbu_script>
   <stream_processing>
	<spstream module="SiteFinder">
		<strand>=</strand>
		<iupac_seq>NNNNNNNNNNNNNNNNNNNNNGG</iupac_seq>
	</spstream>
   </stream_processing>
</zenbu_script>

here is how to find EcoR1 sites

<zenbu_script>
   <stream_processing>
	<spstream module="SiteFinder">
		<strand>=</strand>
		<iupac_seq>GAATTC</iupac_seq>
	</spstream>
   </stream_processing>
</zenbu_script>