BITACORA

BITACORA integrates sequence similarity-based search tools and Perl scripts to annotate and curate gene family members directly from genomic DNA sequences, improving gene family annotation in non-model organisms.

Key Features:

• Integration of sequence similarity-based tools and Perl scripts: Combines sequence similarity-based search tools with Perl scripts to perform similarity searches and downstream curation.
• Curative functionality: Identifies and corrects fused, chimeric, partial, or absent gene models in existing annotations.
• Identification of undetected gene copies: Detects previously undetected gene family copies directly from genomic DNA sequences.
• Output formats: Generates General Feature Format (GFF) and FASTA files containing curated existing gene models and newly identified gene family members.

Scientific Applications:

• Large gene family annotation: Enables comprehensive study of large gene families within fragmented or incomplete genome assemblies.
• Chemosensory gene family analysis: Applied to chemosensory gene families across seven genome sequences, detecting thousands of new chemoreceptors.
• Annotation benchmarking and evolutionary studies: Improves annotations relative to augustus-ppx and supports evolutionary analyses of gene family diversity.

Methodology:

Uses sequence similarity-based searches and Perl scripts to identify and correct inaccuracies in existing annotations and to detect new gene family copies directly from genomic sequences.