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microseq (version 2.1.7)

Basic Biological Sequence Handling

Description

Basic functions for microbial sequence data analysis. The idea is to use generic R data structures as much as possible, making R data wrangling possible also for sequence data.

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Install

install.packages('microseq')

Monthly Downloads

637

Version

2.1.7

License

GPL-2

Issues

2

Pull Requests

0

Stars

3

Forks

1

Maintainer

Lars Snipen

Last Published

September 18th, 2025

Functions in microseq (2.1.7)

translate

Translation according to the standard genetic code
findOrfs

Finding ORFs in genomes
findGenes

Finding coding genes
backTranslate

Replace amino acids with codons
findrRNA

Finding rRNA genes
msa2mat

Convert alignment to matrix
gff2fasta

Retrieving annotated sequences
gregexpr

Extended gregexpr with substring retrieval
microseq

Basic Biological Sequence Analysis
lorfs

Longest ORF
iupac2regex

Ambiguity symbol conversion
msaTrim

Trimming multiple sequence alignments
readGFF

Reading and writing GFF-tables
muscle

Multiple alignment using MUSCLE
reverseComplement

Reverse-complementation of DNA
msalign

Multiple alignment
orfLength

Length of ORF
readFasta

Read and write FASTA files
orfSignature

Signature for each ORF
readFastq

Read and write FASTQ files