lncEvo

lncEvo performs transcriptome assembly from RNA-Seq, predicts long noncoding RNAs (lncRNAs; >200 nucleotides and lacking protein-coding potential), and compares lncRNA transcriptomes between species to identify orthologous lncRNAs and assess their evolutionary conservation.

Key Features:

• Transcriptome assembly from RNA-Seq: Assembles transcriptomes from RNA sequencing (RNA-Seq) data to capture expressed transcripts within samples.
• Prediction of long noncoding RNAs: Predicts lncRNAs and distinguishes them from other transcripts based on sequence features and coding potential.
• Conservation study: Conducts genome-wide comparisons of lncRNA transcriptomes between two species to identify orthologous lncRNAs.
• Modular flexibility: Permits running transcriptome assembly or lncRNA prediction modules independently of the conservation study.
• Customizable parameters: Offers configurable trade-offs between speed and sensitivity for analyses.
• Built-in reporting functionalities: Produces integrated reports summarizing analysis results and outputs.

Scientific Applications:

• Gene regulatory studies: Identifies lncRNAs and assesses their conservation to investigate roles in gene regulation.
• Disease research: Links specific lncRNAs to human diseases to provide insights into molecular mechanisms and disease associations.
• Evolutionary biology: Compares lncRNA transcriptomes across species to study the evolution and diversification of lncRNAs.

Methodology:

Implemented in the Nextflow framework, lncEvo assembles transcriptomes from RNA-Seq, predicts lncRNAs using computational algorithms, and performs genome-wide interspecies comparisons to identify orthologous lncRNAs.