CPGAVAS2

CPGAVAS2 annotates and analyzes plastome sequences by identifying genes, repeats, polymorphisms, and RNA-editing sites using curated plastome reference datasets.

Key Features:

• Reference-Based Plastome Annotation: Annotates plastome sequences using reference datasets including 43 validated plastomes corrected with RNA-seq data and 2,544 curated plastomes refined by sequence alignment.
• Small Exon and Trans-Splicing Gene Detection: Implements specialized algorithms for accurate annotation of small exons in genes such as petB, petD, and rps16, and the trans-splicing gene rps12.
• Genome Feature Identification: Detects genomic features including tandem repeats and dispersed repeat elements within plastome sequences.
• Plastome Diversity Analysis: Provides modules for analyzing sequence diversity among plastomes.
• Polymorphism and RNA-Editing Detection: Identifies single-nucleotide polymorphisms (SNPs) and RNA-editing sites using DNA-seq and RNA-seq datasets.

Scientific Applications:

• Plastid Genome Annotation: Annotates genes and structural elements within chloroplast genomes.
• Comparative Plastome Genomics: Analyzes sequence diversity and structural variation across plastome datasets.
• Plant Evolutionary Genomics: Supports phylogenetic and evolutionary studies using plastid genome sequences.
• RNA Editing and Polymorphism Analysis: Detects RNA-editing events and genetic variation in plastid genomes.

Methodology:

CPGAVAS2 performs plastome annotation using curated plastome reference datasets and specialized algorithms for small exon and trans-splicing gene detection, identifies repeat elements, and analyzes DNA-seq and RNA-seq data to detect SNPs and RNA-editing sites.