AnnotationBustR: an R package to extract subsequences from GenBank annotations

Area of Science:

• Genomics
• Bioinformatics
• Molecular Biology

Background:

• DNA sequences are fundamental to biological research, with large databases like GenBank offering vast resources.
• Extracting specific gene subsequences from GenBank is challenging due to inconsistent gene annotations and numerous synonyms.
• Current methods lack efficiency for large-scale subsequence extraction based on variable gene names.

Purpose of the Study:

• To develop a user-friendly tool for extracting DNA subsequences from GenBank records.
• To address the challenges posed by inconsistent gene annotations and naming conventions in large sequence databases.

Main Methods:

• Introduction of the R package AnnotationBustR.
• Utilizing the ACNUC retrieval system for sequence extraction.
• Employing gene synonyms and accession numbers as search parameters.

Main Results:

• AnnotationBustR enables the extraction of specific DNA subsequences based on GenBank annotations.
• The package generates FASTA files containing the extracted subsequences.
• It facilitates the retrieval of sequences even when gene names vary extensively.

Conclusions:

• AnnotationBustR provides an efficient method for obtaining subsequences from GenBank accessions.
• The generated FASTA files and accession tables streamline downstream analyses, including phylogenetic construction.
• This tool supports ecological and evolutionary hypothesis testing through accessible sequence data.