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microseq

Basic Biological Sequence Handling

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.

Functions (19)

backTranslate

Replace amino acids with codons

findGenes

Finding coding genes

findOrfs

Finding ORFs in genomes

findrRNA

Finding rRNA genes

gff2fasta

Retrieving annotated sequences

gregexpr

Extended gregexpr with substring retrieval

iupac2regex

Ambiguity symbol conversion

lorfs

Longest ORF

microseq-package

Basic Biological Sequence Analysis

msa2mat

Convert alignment to matrix

msaTrim

Trimming multiple sequence alignments

msalign

Multiple alignment

muscle

Multiple alignment using MUSCLE

orfLength

Length of ORF

readFasta

Read and write FASTA files

readFastq

Read and write FASTQ files

readGFF

Reading and writing GFF-tables

reverseComplement

Reverse-complementation of DNA

translate

Translation according to the standard genetic code

microseq

Basic Biological Sequence Handling

v2.1.4

GPL-2

Authors

Lars Snipen, Kristian Hovde Liland

Initial release

2021-01-25

microseq

Functions (19)

microseq

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