DECIPHER (software)

DECIPHER is a software that can be used to decipher and manage biological sequences efficiently using the programming language R.

Features

Sequence databases: import, maintain, view, and export, and interact with a massive number of sequences.
Homology finding: rapidly query sequences for homologous hits among a set of target sequences or genomes. Cluster into groups of related sequences.
Multiple sequence alignment: align sequences of DNA, RNA, or amino acids.
Genome alignment: find and align the syntenic regions of multiple genomes.
Oligonucleotide design: primer design for polymerase chain reaction (PCR), probe design for fluorescence in situ hybridization (FISH) or DNA microarrays.
Manipulate sequences: trim low quality regions, correct frameshifts, reorient nucleotides, determine consensus, or digest with restriction enzymes.
Analyze sequences: find chimeras, detect repeats, predict secondary structure, classify into a taxonomy of organisms or functions, create phylogenetic trees, and ancestral reconstruction.
Gene finding: predict coding and non-coding genes in a genome, extract them from the genome, and export them to a file.