Basic Biological Sequence Handling
Multiple alignment
Read and write FASTQ files
Replace amino acids with codons
Finding coding genes
Finding ORFs in genomes
Finding rRNA genes
Retrieving annotated sequences
Extended gregexpr with substring retrieval
Ambiguity symbol conversion
Longest ORF
Basic Biological Sequence Analysis
Convert alignment to matrix
Trimming multiple sequence alignments
Multiple alignment using MUSCLE
Length of ORF
Signature for each ORF
Read and write FASTA files
Reading and writing GFF-tables
Reverse-complementation of DNA
Translation according to the standard genetic code
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.