MICheck

MICheck verifies annotated genes and detects frameshifts in bacterial genomes by assessing coding potential and nucleotide composition heterogeneity to improve annotation accuracy.

Key Features:

• Automated verification: Automates checking of annotated genes and identification of potential frameshift errors in bacterial genomes.
• Coding potential and nucleotide composition analysis: Assesses coding potential and nucleotide composition heterogeneity to distinguish authentic protein-coding genes from false positives and to detect overlooked genes.
• Graphical genomic-context representation: Produces graphical representations of genomic context including coding potential curves and neighboring gene annotations.
• Benchmarking on RefSeq genomes: Demonstrated on 20 bacterial genomes, including nine entries with 'Reviewed' status from NCBI RefSeq.

Scientific Applications:

• Genome re-annotation quality control: Serves as a preliminary verification step in microbial genome re-annotation projects to identify missing or incorrectly annotated genes before functional re-annotation.
• Public database curation: Aids verification of genomic data integrity in public databases such as NCBI RefSeq.
• Annotation error and frameshift detection: Detects frameshifts and annotation discrepancies to guide curation and correction of bacterial gene annotations.

Methodology:

Systematic automated analysis of gene annotations leveraging coding potential metrics and nucleotide composition heterogeneity to identify discrepancies and predicted frameshifts.