ICAnnoLncRNA

ICAnnoLncRNA identifies, classifies, and annotates long non-coding RNAs (lncRNAs) within assembled transcriptomic sequences to support discovery and characterization of lncRNAs, defined as RNA molecules exceeding 200 nucleotides that do not encode proteins.

Key Features:

• Automated Workflow: Executes end-to-end processing of transcriptomic data through the pipeline without manual orchestration of intermediate steps.
• Integration with LncFinder: Utilizes LncFinder software for lncRNA identification with adjustable recognition parameters based on annotated genomic data.
• Prediction and Filtering: Predicts candidate lncRNAs and filters out erroneous transcripts and probable transposable elements.
• Genome Alignment: Aligns identified lncRNA sequences to a reference genome for genomic localization.
• Classification by Genome Location: Classifies lncRNAs according to their genomic positions to inform functional interpretation.
• Database Comparison: Compares lncRNA sequences against external databases to refine annotation and detect novel features.
• Structural and Expression Analysis: Assesses structural characteristics of lncRNAs and evaluates their expression profiles.

Scientific Applications:

• Cross-species lncRNA discovery: Facilitates identification and comparative analysis of lncRNAs across multiple species, including non-plant taxa.
• Functional and regulatory studies: Supports research into diverse functions and regulatory roles of lncRNAs via localization, annotation, and expression analyses.

Methodology:

Uses LncFinder for identification, predicts and filters lncRNA candidates including probable transposable elements, aligns sequences to a reference genome, and was applied to transcriptomic sequences from 15 maize libraries assembled using Trinity, Hisat2, and StringTie.