CYCLeR

CYCLeR assembles and quantifies circular RNA (circRNA) transcripts from RNA-seq data, determining full sequence identities and alternative splicing isoforms involving back-splice junctions (BSJs).

Key Features:

• Full Sequence Identification: Determines complete sequence identity of novel and alternatively spliced circRNAs arising from the same BSJ.
• Simultaneous Quantification: Co-estimates abundances of circRNAs and known linear splicing isoforms from RNA-seq data.
• Output Formats: Produces FASTA, GTF, and flat annotation files and a padded FASTA index for transcript expression estimation using Expectation-Maximization (EM) algorithms.
• Performance Superiority: Demonstrates higher F-score and improved transcript quantification accuracy on simulated data and is validated against long-read sequencing data.
• Biological Insights: Reveals circRNA expression patterns in Drosophila melanogaster datasets that are not detected by other tools.

Scientific Applications:

• CircRNA discovery and isoform resolution: Identification and sequence-level characterization of novel circRNAs and alternatively spliced circRNA isoforms.
• Transcript quantification: Quantification of circRNA and linear splicing isoform abundances for comparative expression analyses.
• Gene regulation and disease studies: Investigating gene regulation mechanisms and roles of circRNAs in disease pathogenesis.
• Evolutionary and splicing mechanism studies: Studying evolutionary aspects and non-canonical splicing events involving BSJs.
• Benchmarking and validation: Benchmarking circRNA detection and quantification methods using simulated data and long-read sequencing comparisons.

Methodology:

Assembles circRNA transcripts from RNA-seq, identifies alternative splicing isoforms involving BSJs, co-estimates abundances of circRNAs and linear isoforms, outputs FASTA/GTF/flat annotation files and a padded FASTA used as an index for EM-based expression estimation, and is evaluated using simulated data and long-read sequencing comparisons.