ALGAEFUN

ALGAEFUN performs functional enrichment and target-gene identification for microalgae by analyzing RNA-seq and ChIP-seq data to interpret transcriptomic and cistromic signals.

Key Features:

• MARACAS (MicroAlgae RnA-seq and Chip-seq AnalysiS): MARACAS provides an automated computational pipeline to process raw RNA-seq and ChIP-seq data, generate sets of differentially expressed genes from RNA-seq, and identify genomic loci from ChIP-seq.
• ALGAEFUN (microALGAE FUNctional enrichment tool): ALGAEFUN performs Gene Ontology and biological pathway enrichment analyses on gene sets, identifies potential target genes from ChIP-seq loci, and analyzes the distribution of loci across gene features.
• Graphical output and export: Generates graphical representations and downloadable tables with detailed gene annotations to support interpretation and downstream analysis.

Scientific Applications:

• Molecular mechanism analysis: Enables decoding molecular mechanisms underlying microalgal physiology and compound biosynthesis using transcriptomic and cistromic data.
• Biotechnological optimization: Supports optimization of microalgae as cell-factories for biofuels, agricultural biostimulants, soil bioremediation, and nutritional supplements by linking omics signals to functional pathways and targets.

Methodology:

Integration of MARACAS for initial processing of raw RNA-seq and ChIP-seq data to produce differentially expressed genes and genomic loci, together with ALGAEFUN for Gene Ontology and pathway enrichment, target gene identification, locus distribution analysis, and generation of graphical outputs and tables.