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Overview

DECIPHER is a software toolset that can be used for deciphering and managing biological sequences efficiently using the R programming language. The R package is distributed as platform independent source code under the GPL version 3 license. Some functionality of the program is accessible online through web tools.

Installation

To install DECIPHER, start the latest version of R and enter:
if (!requireNamespace("BiocManager", quietly=TRUE))
    install.packages("BiocManager")
BiocManager::install("DECIPHER")
Visit the Tutorials page to learn how you can get started DECIPHERing. Questions can be posted on the Bioconductor Support forum.

Features

  • Sequence databases: import, maintain, view, and export a massive number of sequences.
  • Sequence alignment: accurately align thousands of DNA, RNA, or amino acid sequences. Quickly find and align the syntenic regions of multiple genomes.
  • Oligo design: test oligos in silico, or create new primer and probe sequences optimized for a variety of objectives.
  • Manipulate sequences: trim low quality regions, correct frameshifts, reorient nucleotides, determine consensus, or digest with restriction enzymes.
  • Analyze sequences: find chimeras, classify into a taxonomy of organisms or functions, detect repeats, predict secondary structure, create phylogenetic trees, and reconstruct ancestral states.
  • Gene finding: predict coding and non-coding genes in a genome, extract them from the genome, and export them to a file.