Basic Biological Sequence Handling

Documentation for package ‘microseq’ version 1.3

microseq-package	Basic Biological Sequence Analysis
Fasta	Read and write FASTA files
findGenes	Finding coding genes
findOrfs	Finding ORFs in genomes
findrRNA	Finding rRNA genes
gff2fasta	Retrieving annotated sequences
gffSignature	GFF signature text
gregexpr	Extended 'gregexpr' with substring retrieval
iupac2regex	Ambiguity symbol conversion
lorfs	Longest ORF
microseq	Basic Biological Sequence Analysis
msalign	Multiple alignment
msaTrim	Trimming multiple sequence alignments
muscle	Multiple alignment using MUSCLE
orfLength	ORF lengths
plot.Fasta	Plotting and summary of 'Fasta' objects
plot.Fastq	Plotting and summary of 'Fastq' objects
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
summary.Fasta	Plotting and summary of 'Fasta' objects
summary.Fastq	Plotting and summary of 'Fastq' objects
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