mpss

mpss integrates small RNAs, degradome reads (RNA ends), RNA sequencing, and chromatin immunoprecipitation sequencing (ChIP-seq) data across plant genomes to support analysis of small RNA pathways, transcript diversity, and repeat/transposon distributions.

Key Features:

• Comprehensive Data Handling: Manages RNA-derived datasets across a wide range of plant species, including Arabidopsis thaliana and wheat (Triticum spp.).
• Integrated Data Types: Integrates small RNAs, degradome reads (RNA ends), RNA sequencing, and chromatin immunoprecipitation sequencing (ChIP-seq) to correlate molecular abundance with genomic context.
• Novel Transcript Information: Identifies antisense transcripts, alternative splice isoforms, and regulatory intergenic transcripts.
• Phased Small RNA Analysis: Analyzes phased small RNAs to characterize biogenesis and function in plant small RNA pathways.
• Repeat and Transposon Annotation: Annotates repeats and transposons to contextualize small RNAs and transcripts within repetitive genomic elements.

Scientific Applications:

• Small RNA pathway analysis: Enables investigation of small RNA biogenesis, phasing, and regulatory roles in plants using integrated small RNA and degradome data.
• Gene regulation and epigenetics: Supports studies of gene regulation and epigenetic modifications by combining RNA sequencing, degradome, and ChIP-seq data with repeat/transposon annotations.
• Transcriptome complexity: Facilitates identification and characterization of antisense transcripts, alternative splice isoforms, and intergenic regulatory transcripts.
• Comparative plant genomics: Supports cross-species comparisons across model and crop species such as Arabidopsis thaliana and wheat (Triticum spp.).

Methodology:

Integrates diverse genomic datasets and processes data derived from Illumina sequencing technologies.