dipwmsearch

dipwmsearch searches for dinucleotide position weight matrix (di-PWM) motifs in nucleotide sequences to identify putative transcription factor binding sites and other DNA/RNA binding regions.

Key Features:

• Dinucleotide PWM representation: Uses dinucleotide position weight matrices (di-PWMs) to incorporate dependencies between adjacent nucleotides within motifs.
• Enumeration-based search algorithm: Enumerates matching words corresponding to the di-PWM and then searches these words collectively within target sequences.
• Pre-computation of matches: Pre-computes potential di-PWM matches to accelerate sequence scanning.
• Ambiguous nucleotide handling: Supports IUPAC ambiguous nucleotide codes in input sequences during motif search.

Scientific Applications:

• Transcription factor binding site annotation: Identification and annotation of putative transcription factor binding sites in genomic and transcriptomic sequences.
• Regulatory element prediction using experimental di-PWMs: Application of di-PWMs derived from experimental data (e.g., HOCOMOCO) to predict and study regulatory elements involved in gene expression regulation.
• Study of DNA/RNA binding regions: Detection of sequence motifs relevant to DNA- and RNA-binding proteins to support investigations of gene regulation and its implications in health and disease.

Methodology:

Enumerates matching words for a given di-PWM, pre-computes potential matches, then searches these collectively within target sequences, with optimization for IUPAC ambiguous codes; method builds upon algorithmic approaches related to SPRy-SARUS and MOODS.