ALGAEFUN with MARACAS, microALGAE FUNctional enrichment tool for MicroAlgae RnA-seq and Chip-seq AnalysiS

Area of Science:

• Biotechnology
• Bioinformatics
• Marine Biology

Background:

• Microalgae are valuable sustainable resources for biofuels, agriculture, and nutrition.
• Underlying molecular mechanisms in microalgae remain largely uncharacterized, limiting their potential as cell-factories.
• Omics technologies offer insights, but specialized tools for microalgae data analysis are lacking.

Purpose of the Study:

• To provide microalgae researchers with an enabling tool to analyze transcriptomic and cistromic high-throughput sequencing data.
• To facilitate the exploitation of RNA-seq and ChIP-seq data for biological discovery.
• To bridge the gap between raw omics data and meaningful biological insights in microalgae.

Main Methods:

• Development of MARACAS (MicroAlgae RnA-seq and Chip-seq AnalysiS) for automated processing of RNA-seq and ChIP-seq raw data.
• Implementation of ALGAEFUN (microALGAE FUNctional enrichment tool) as a web-based application for functional enrichment analysis.
• Integration of pipelines for differential gene expression analysis, genomic loci identification, Gene Ontology, and pathway enrichment.

Main Results:

• MARACAS generates differentially expressed gene sets (RNA-seq) and genomic loci lists (ChIP-seq).
• ALGAEFUN performs functional enrichment analysis on gene sets and ChIP-seq loci, identifying potential target genes.
• Both tools provide graphical representations and downloadable tables with gene annotations for further analysis.

Conclusions:

• ALGAEFUN with MARACAS offers an integrated environment for microalgae research.
• The tools facilitate the interpretation of gene lists and genomic loci through functional enrichment analysis.
• ALGAEFUN with MARACAS is publicly available to support the microalgae research community.