LASAGNA-Search

LASAGNA-Search identifies transcription factor binding sites (TFBSs) in genomic sequences and supports gene regulatory network inference, providing analysis complementary to ChIP-seq datasets such as ENCODE and modENCODE.

Key Features:

• Length-Aware Site Alignment (LASAGNA): Uses the LASAGNA (Length-Aware Site Alignment Guided by Nucleotide Association) algorithm to accommodate unaligned TFBSs of variable lengths.
• Comprehensive TF model collection: Contains a repository of 1,726 transcription factor models for scanning and comparison.
• Automatic promoter sequence retrieval: Retrieves promoter sequences automatically for downstream TFBS searches.
• Visualization integration: Integrates results with the UCSC Genome Browser for genomic-context visualization.
• Gene regulatory network inference and visualization: Infers and visualizes gene regulatory networks based on binding specificities.

Scientific Applications:

• TFBS identification in unannotated sequences: Detects potential TFBSs in sequences lacking annotation, including for lesser-known transcription factors and non-model organisms without extensive ChIP-seq data.
• Complementary analysis to ChIP-seq: Provides computational TFBS predictions that complement experimental ChIP-seq datasets such as ENCODE and modENCODE.
• Gene regulatory network reconstruction: Supports construction and visualization of regulatory networks from predicted binding specificities.
• Studying transcriptional regulation and disease-related interactions: Facilitates analysis of transcriptional regulatory mechanisms and their potential links to biological processes and disease.

Methodology:

Implements the LASAGNA algorithm (Length-Aware Site Alignment Guided by Nucleotide Association) for variable-length TFBS alignment, performs automatic promoter sequence retrieval, and integrates results with the UCSC Genome Browser for visualization.