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 |