Documentation for Motif Analysis Interface

This documentation provides a detailed explanation of the different functionalities and configurable parameters in the motif analysis interface.

Step 2.1: Sequences

• Users can extract (see: Promoter and Terminator Extraction) or input a list of sequences in FASTA format. (see: Understand FASTA sequence)

Step 2.2 - 2.3: Motif Type

The tool supports three types of motif definitions:

1. Individual Motif:
   • Input using the IUPAC nucleotide code (e.g., R for purines, Y for pyrimidines, etc.).
   • Example: GGGRNYCCC.
   • IUPAC Code:
2. JASPAR ID:
   • Use the unique identifier of a motif from the JASPAR database.
   • Exemple
3. Position Weight Matrix (PWM):
   • A matrix of nucleotide probabilities for each position in the motif.
   • Users can:
     • Input a pre-existing PWM.
       • How to build your PWM ?
     • Create a PWM from multiple FASTA sequences using the tool.
       • How to build your PWM using FASTA sequence ?

Step 2.4: Transcription Start Site (TSS) or Gene End

• Set the distance relative to the TSS or gene end, in base pairs (bp) (see: Understand FASTA sequence). If Promoter and Terminator Extraction is used, it is defined automatically (and corresponding to “Upstream”).

Step 2.5: Relative Score Threshold (see also: Mathematical method)

• Defines the Relative Score threshold for motif matching.