Tbl2KnownGene

Tbl2KnownGene converts NCBI .tbl annotation files into UCSC knownGene.txt annotation tables for use in genomic analyses.

Key Features:

• Format Conversion: Parses NCBI .tbl files and generates corresponding UCSC knownGene.txt annotation tables.
• Schema Compatibility: Produces output aligned with the UCSC Known Genes schema to maintain compatibility with tools expecting knownGene.txt.
• Model Organism Utility: Generates knownGene.txt files from existing .tbl annotations for model organisms such as Arabidopsis (TAIR10).

Scientific Applications:

• Genomic Research: Facilitates integration and analysis of genomic annotations by converting .tbl to knownGene.txt for cross-platform workflows.
• Custom Analysis Tools: Provides standardized knownGene.txt output required by downstream analysis tools that consume UCSC Known Genes format.
• Cross-Species Applicability: Applicable to organisms with NCBI .tbl annotations, including Arabidopsis datasets (TAIR10), enabling use across diverse genomic studies.

Methodology:

Parses NCBI .tbl files to generate UCSC knownGene.txt tables; implemented as a Perl script; algorithm tested using chromosome datasets from the Arabidopsis genome (TAIR10).