Learn R Programming

AnnotationBustR (version 1.3.0)

Extract Subsequences from GenBank Annotations

Description

Extraction of subsequences into FASTA files from GenBank annotations where gene names may vary among accessions. Borstein & O'Meara (2018) .

Copy Link

Version

Install

install.packages('AnnotationBustR')

Monthly Downloads

431

Version

1.3.0

License

GPL (>= 2)

Issues

Pull Requests

Stars

Forks

Repository

https://github.com/sborstein/AnnotationBustR

Homepage

https://www.ncbi.nlm.nih.gov/nuccore

Maintainer

Samuel Borstein

Last Published

September 24th, 2020

Functions in AnnotationBustR (1.3.0)

AnnotationBustR

An R package to extract sub-sequences from GenBank annotations under different synonyms

Breaks up genbank sequences into their annotated components based on a set of search terms and writes each subsequence of interest to a FASTA for each accession number supplied.

Ribosomal DNA (rDNA) Search Terms

MergeSearchTerms

Merging of two tables containing search terms to expand search term database for the AnnotationBust function.

Find the longest sequence for each species from a list of GenBank accession numbers.

Chloroplast DNA (cpDNA) Search Terms

Mitochondrial DNA Search Terms for Animals

mtDNAtermsPlants

Mitochondrial DNA Search Terms for Plants