Cyanorak

Cyanorak curates and organizes genomic sequences and orthologous clusters for Prochlorococcus, Synechococcus, and Cyanobium to support comparative genomics and functional annotation.

Key Features:

• Database content: Sequences from 97 genomes are organized into 25,834 likely orthologous groups (CLOGs).
• Search indexing: Gene names and product terms are indexed to retrieve relevant CLOGs and individual gene entries.
• Functional annotation: CLOGs are annotated with EggNOG, EC/K numbers, Gene Ontology (GO) terms, TIGR Roles, Cyanorak Roles, and protein motif predictions.
• Phyletic profiles: Phyletic profiles record genotype and pigment type for each CLOG.
• Genome visualization (JBrowse): JBrowse integration provides genome tracks for predicted operons, genomic islands, and transcriptomic data.
• BLAST sequence search: BLAST is available for sequence alignment and homology detection across the genome collection.
• Comparative genomic contexts: Genomic context views facilitate analysis of evolutionary relationships and functional conservation.
• Strain locality mapping: An interactive map links strains to their isolation sites for geographic context.
• Data export: Data export options enable downloading datasets for external analyses.

Scientific Applications:

• Comparative genomics: Identification and comparison of orthologous gene clusters across Prochlorococcus, Synechococcus, and Cyanobium.
• Functional annotation and metabolic inference: Aggregated annotations (EggNOG, EC/K, GO, TIGR, Cyanorak Roles, motifs) support prediction of gene functions and pathways.
• Phylogenetics and evolutionary analyses: Phyletic profiles and comparative contexts support studies of evolutionary relationships and pigment-type adaptations.
• Ecology and biogeography: Strain isolation site mapping combined with genotype and pigment data supports ecological distribution and biogeographical studies.
• Transcriptomic integration: Genome tracks for transcriptomic data enable linking expression patterns to genomic features.

Methodology:

Sequences from 97 genomes are organized into 25,834 likely orthologous groups (CLOGs); functional annotations include EggNOG, EC/K numbers, Gene Ontology (GO) terms, TIGR Roles, Cyanorak Roles, and protein motif predictions; phyletic profiles record genotype and pigment type per CLOG; JBrowse is integrated for predicted operons, genomic islands, and transcriptomic tracks; BLAST is provided for sequence alignment and homology searches; an interactive map links strains to isolation sites and data export options enable external analyses.