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AnnotationBustR: an R package to extract subsequences from GenBank annotations.

Samuel R Borstein1, Brian C O'Meara1

  • 1Department of Ecology & Evolutionary Biology, University of Tennessee, Knoxville, TN, USA.

Peerj
|July 14, 2018
PubMed
Summary
This summary is machine-generated.

AnnotationBustR simplifies DNA sequence extraction from GenBank, overcoming annotation inconsistencies. This R package facilitates comparative analyses by providing FASTA files of targeted subsequences.

Keywords:
ACNUCDNA barcodesGenBankPhylogeneticsR PackageSequence dataSubsequencescpDNAmtDNA

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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.