Basic Biological Sequence Handling


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Documentation for package ‘microseq’ version 2.1.6

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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