Package: AnnotationBustR 2.0

AnnotationBustR: Extract Subsequences from GenBank Annotations

Extraction of subsequences into FASTA files from GenBank annotations where gene names may vary among accessions. Borstein & O'Meara (2018) <doi:10.7717/peerj.5179>.

Authors:Samuel R. Borstein [aut, cre], Brian O'Meara [aut]

AnnotationBustR_2.0.tar.gz
AnnotationBustR_2.0.zip(r-4.7-any)AnnotationBustR_2.0.zip(r-4.6-any)AnnotationBustR_2.0.zip(r-4.5-any)
AnnotationBustR_2.0.tgz(r-4.6-any)AnnotationBustR_2.0.tgz(r-4.5-any)
AnnotationBustR_2.0.tar.gz(r-4.7-any)AnnotationBustR_2.0.tar.gz(r-4.6-any)
AnnotationBustR_2.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
AnnotationBustR/json (API)

# Install 'AnnotationBustR' in R:

install.packages('AnnotationBustR', repos = c('https://sborstein.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/sborstein/annotationbustr/issues

Pkgdown/docs site:https://sborstein.github.io

Datasets:

cpDNAterms - Chloroplast DNA (cpDNA) Search Terms
mtDNAterms - Mitochondrial DNA Search Terms for Animals
mtDNAtermsPlants - Mitochondrial DNA Search Terms for Plants
rDNAterms - Ribosomal DNA (rDNA) Search Terms

On CRAN:

5.39 score 5 stars 11 scripts 1.3k downloads 1 mentions 3 exports 70 dependencies

Last updated from:0dd6ffbd06. Checks:9 OK. Indexed: yes.

Target	Result	Time
linux-devel	OK	318
source / vignettes	OK	354
linux-release	OK	219
macos-release	OK	351
macos-oldrel	OK	278
windows-devel	OK	220
windows-release	OK	204
windows-oldrel	OK	209
wasm-release	OK	125

Exports:AnnotationBust FindLongestSeq MergeSearchTerms

Dependencies:AnnotationDbi askpass BH Biobase BiocBaseUtils BiocGenerics BiocIO BiocParallel Biostrings bit bit64 bitops blob BSgenome cachem cigarillo cli codetools cpp11 crayon curl DBI dplyr fastmap formatR futile.logger futile.options generics GenomicAlignments GenomicFeatures GenomicRanges glue httr IRanges jsonlite KEGGREST lambda.r lifecycle magrittr matrixStats memoise mime openssl pillar pkgconfig png R6 RCurl rentrez restfulr Rhtslib rjson rlang Rsamtools RSQLite rtracklayer S4Vectors Seqinfo snow stringi stringr sys tibble tidyselect utf8 vctrs withr XML XVector yaml

AnnotationBustR Tutorial

Rendered fromAnnotationBustR-vignette.Rmdusingknitr::rmarkdown

Last update: 2026-08-30
Started: 2016-05-25

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
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.	AnnotationBust
An R package to extract sub-sequences from GenBank annotations under different synonyms	AnnotationBustR
Chloroplast DNA (cpDNA) Search Terms	cpDNAterms
Find the longest sequence for each species from a list of GenBank accession numbers.	FindLongestSeq
Merging of two tables containing search terms to expand search term database for the AnnotationBust function.	MergeSearchTerms
Mitochondrial DNA Search Terms for Animals	mtDNAterms
Mitochondrial DNA Search Terms for Plants	mtDNAtermsPlants
Ribosomal DNA (rDNA) Search Terms	rDNAterms