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microseq (version 2.1.5)

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

587

Version

2.1.5

License

GPL-2

Maintainer

Lars Snipen

Last Published

October 30th, 2021

Functions in microseq (2.1.5)

findOrfs

Finding ORFs in genomes
gregexpr

Extended gregexpr with substring retrieval
muscle

Multiple alignment using MUSCLE
orfLength

Length of ORF
gff2fasta

Retrieving annotated sequences
translate

Translation according to the standard genetic code
findrRNA

Finding rRNA genes
readFasta

Read and write FASTA files
readFastq

Read and write FASTQ files
iupac2regex

Ambiguity symbol conversion
lorfs

Longest ORF
msa2mat

Convert alignment to matrix
msaTrim

Trimming multiple sequence alignments
microseq-package

Basic Biological Sequence Analysis
msalign

Multiple alignment
readGFF

Reading and writing GFF-tables
reverseComplement

Reverse-complementation of DNA
findGenes

Finding coding genes
backTranslate

Replace amino acids with codons