BAGET

BAGET extracts gene and protein sequences and displays genomic context from fully sequenced prokaryotic genomes (bacteria and archaea) to support molecular genetics and phylogenetic analyses.

Key Features:

• Gene and Protein Sequence Extraction: Queries and retrieves DNA and protein sequences from fully sequenced prokaryotic genomes.
• Dynamic Visual Gene Context Information: Provides two levels of visual context on a single page: a graphical representation of a user-defined chromosomal region centered on the target gene, and the DNA sequence of the query gene with neighboring genes and intergenic regions, color-coded.
• Amino Acid Sequence Provision: Outputs corresponding amino acid sequences for protein-coding genes.
• Export Functionality: Exports query results as rich text format (RTF) files.

Scientific Applications:

• Comparative Genomics: Enables sequence retrieval and contextual comparisons across bacterial and archaeal genomes for comparative analyses.
• Phylogenetic Analysis: Provides DNA and amino acid sequences suitable for phylogenetic inference and tree construction.
• Functional Annotation: Supports functional annotation of genes by supplying sequences and genomic neighborhood information.

Methodology:

Integrates graphical chromosomal displays with sequence-based outputs (DNA and amino acid sequences) to present comprehensive gene context information.