DECIPHER (software)
From Wikipedia, the free encyclopedia
DECIPHER is a software that can be used to decipher and manage biological sequences efficiently using the programming language R.
DeveloperErik Wright
Stable release
3.4.0
/ 2025
| DECIPHER | |
|---|---|
| Developer | Erik Wright |
| Stable release | 3.4.0
/ 2025 |
| Written in | R, C |
| Operating system | Unix, Linux, macOS, Windows |
| Platform | x86-64, ARM |
| Available in | English |
| Type | Bioinformatics |
| License | GPL 3 |
| Website | decipher |
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.[1]
- Multiple sequence alignment: align sequences of DNA, RNA,[2] or amino acids.[3]
- Genome alignment: find and align the syntenic regions of multiple genomes.
- Oligonucleotide design:[4] primer design[5][6] for polymerase chain reaction (PCR), probe design for fluorescence in situ hybridization (FISH)[7] or DNA microarrays.[8]
- Manipulate sequences: trim low quality regions, correct frameshifts, reorient nucleotides, determine consensus, or digest with restriction enzymes.
- Analyze sequences: find chimeras,[9] detect repeats, predict secondary structure, classify into a taxonomy of organisms[10] or functions,[11] create phylogenetic trees, and ancestral reconstruction.
- Gene finding: predict coding and non-coding genes[12] in a genome, extract them from the genome, and export them to a file.
