meme_fimo

meme_fimo scans DNA and protein sequences using position-specific scoring matrices (PSSMs) to identify motif occurrences and assess their statistical significance.

Key Features:

• Motif scanning: Scans sequence databases using position-specific scoring matrices (PSSMs) to locate motif occurrences in DNA and protein sequences.
• Log-likelihood scoring: Computes a log-likelihood ratio score at each position in the sequence database.
• P-value calculation: Uses dynamic programming to convert log-likelihood scores into P-values.
• False discovery rate analysis: Estimates q-values to control for multiple hypothesis testing.
• Output formats: Produces results in HTML, XML, and Santa Cruz Genome Browser formats.
• Performance: Scans DNA sequences at approximately 3.5 megabases per second on a single CPU.
• MEME Suite integration: Is part of the MEME Suite.
• High-throughput readiness: Suitable for large-scale analyses and datasets generated by high-throughput sequencing technologies.

Scientific Applications:

• Motif-based sequence analysis: Used in pipelines to identify and characterize functional elements in genomic and proteomic data.
• Regulatory and protein-binding motif identification: Detects occurrences of regulatory and protein-binding motifs in DNA and protein sequences.
• High-throughput sequencing analysis: Applied to large datasets produced by high-throughput sequencing technologies for motif discovery and annotation.

Methodology:

Scans sequences with PSSMs, computes log-likelihood ratio scores at each position, applies dynamic programming to derive P-values, and performs false discovery rate analysis to estimate q-values.