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microseq (version 2.1.6)

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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Version

Install

install.packages('microseq')

Monthly Downloads

618

Version

2.1.6

License

GPL-2

Maintainer

Lars Snipen

Last Published

August 21st, 2023

Functions in microseq (2.1.6)

backTranslate

Replace amino acids with codons
readGFF

Reading and writing GFF-tables
muscle

Multiple alignment using MUSCLE
orfSignature

Signature for each ORF
msaTrim

Trimming multiple sequence alignments
orfLength

Length of ORF
msalign

Multiple alignment
reverseComplement

Reverse-complementation of DNA
readFastq

Read and write FASTQ files
translate

Translation according to the standard genetic code
readFasta

Read and write FASTA files
microseq-package

Basic Biological Sequence Analysis
iupac2regex

Ambiguity symbol conversion
gregexpr

Extended gregexpr with substring retrieval
findrRNA

Finding rRNA genes
gff2fasta

Retrieving annotated sequences
lorfs

Longest ORF
findGenes

Finding coding genes
findOrfs

Finding ORFs in genomes
msa2mat

Convert alignment to matrix