Basic Biological Sequence Handling

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Documentation for package ‘microseq’ version 2.1.6

• DESCRIPTION file.
• User guides, package vignettes and other documentation.

Help Pages

microseq-package	Basic Biological Sequence Analysis
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	Basic Biological Sequence Analysis
msa2mat	Convert alignment to matrix
msalign	Multiple alignment
msaTrim	Trimming multiple sequence alignments
muscle	Multiple alignment using MUSCLE
orfLength	Length of ORF
orfSignature	Signature for each ORF
readFasta	Read and write FASTA files
readFastq	Read and write FASTQ files
readGFF	Reading and writing GFF-tables
regex2iupac	Ambiguity symbol conversion
reverseComplement	Reverse-complementation of DNA
translate	Translation according to the standard genetic code
writeFasta	Read and write FASTA files
writeFastq	Read and write FASTQ files
writeGFF	Reading and writing GFF-tables