PCIR

PCIR identifies and catalogs inverted repeats (IRs) in plant chloroplast genomes to support analysis of IR distribution, associated genes, marker mapping, and phylogenetic relationships.

Key Features:

• Extensive datasets: Contains 21,433 IRs across 113 plant chloroplast genomes, 16,948 functional genes, and 21,659 visual maps.
• IR prediction: Predicts inverted repeats from chloroplast DNA sequences to identify IR nucleotides and junction sites.
• Search and visualization: Provides search capabilities and generation of visual maps for IR locations and junctions.
• Phylogenetic analysis: Enables analysis of phylogenetic relationships using IR information across different species.
• Marker maps: Produces high-quality marker maps for genomic studies and marker identification related to IRs.

Scientific Applications:

• IR distribution and architecture: Comparative analysis of IR distribution patterns and structural features within chloroplast genomes.
• Functional gene annotation: Annotation and investigation of functional genes associated with IR regions (16,948 genes in the dataset).
• Genomic instability and replication studies: Investigation of roles of IRs in genomic instability and DNA replication processes.
• Phylogenetics and comparative genomics: Use of IR-based data to infer evolutionary relationships and perform comparative genomics across plant species.

Methodology:

Uses sequenced chloroplast genome data to predict and detect inverted repeats from chloroplast DNA sequences, search and visualize IRs and junction sites, generate marker maps, and perform phylogenetic analysis using IR information.