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 Multiple sequence alignment (MSA) is the process or the result of sequence alignment of three or more biological sequences, generally protein, DNA, or RNA. These alignments are used to infer evolutionary relationships via phylogenetic analysis an ...

: align sequences of

DNA Deoxyribonucleic acid (; DNA) is a polymer composed of two polynucleotide chains that coil around each other to form a double helix. The polymer carries genetic instructions for the development, functioning, growth and reproduction of al ...

RNA Ribonucleic acid (RNA) is a polymeric molecule that is essential for most biological functions, either by performing the function itself (non-coding RNA) or by forming a template for the production of proteins (messenger RNA). RNA and deoxyrib ...

, or

amino acid Amino acids are organic compounds that contain both amino and carboxylic acid functional groups. Although over 500 amino acids exist in nature, by far the most important are the 22 α-amino acids incorporated into proteins. Only these 22 a ...

s. * Genome alignment: find and align the syntenic regions of multiple genomes. * Oligonucleotide design:

primer Primer may refer to: Arts, entertainment, and media Films * ''Primer'' (film), a 2004 feature film written and directed by Shane Carruth * ''Primer'' (video), a documentary about the funk band Living Colour Literature * Primer (textbook), a te ...

design for

polymerase chain reaction The polymerase chain reaction (PCR) is a method widely used to make millions to billions of copies of a specific DNA sample rapidly, allowing scientists to amplify a very small sample of DNA (or a part of it) sufficiently to enable detailed st ...

(PCR), probe design for

fluorescence in situ hybridization Fluorescence ''in situ'' hybridization (FISH) is a molecular cytogenetic technique that uses fluorescent probes that bind to only particular parts of a nucleic acid sequence with a high degree of sequence complementarity. It was developed by ...

(FISH) or

DNA microarray A DNA microarray (also commonly known as a DNA chip or biochip) is a collection of microscopic DNA spots attached to a solid surface. Scientists use DNA microarrays to measure the expression levels of large numbers of genes simultaneously or t ...

s. * Manipulate sequences: trim low quality regions, correct frameshifts,

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nucleotides, determine consensus, or digest with

restriction enzyme A restriction enzyme, restriction endonuclease, REase, ENase or'' restrictase '' is an enzyme that cleaves DNA into fragments at or near specific recognition sites within molecules known as restriction sites. Restriction enzymes are one class o ...

s. * Analyze sequences: find chimeras, detect repeats, predict

secondary structure Protein secondary structure is the local spatial conformation of the polypeptide backbone excluding the side chains. The two most common Protein structure#Secondary structure, secondary structural elements are alpha helix, alpha helices and beta ...

, classify into a taxonomy of organisms or functions, create

phylogenetic tree A phylogenetic tree or phylogeny is a graphical representation which shows the evolutionary history between a set of species or taxa during a specific time.Felsenstein J. (2004). ''Inferring Phylogenies'' Sinauer Associates: Sunderland, MA. In ...

s, and

ancestral reconstruction Ancestral reconstruction (also known as ''Character Mapping'' or ''Character Optimization'') is the extrapolation back in time from measured characteristics of individuals, populations, or species to their Common descent, common ancestors. It is an ...

. *

Gene finding In computational biology, gene prediction or gene finding refers to the process of identifying the regions of genomic DNA that encode genes. This includes protein-coding genes as well as RNA genes, but may also include prediction of other functio ...

: predict coding and non-coding genes in a genome, extract them from the genome, and export them to a file.

References

External links

* Phylogenetics software {{science-software-stub

Features

See also

References

External links