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.
- 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.
-
^ Wright ES (2024).
"Accurately clustering biological sequences in linear time by relatedness sorting". Nature Communications. 15: 3047.
doi:
10.1038/s41467-024-47371-9.
PMC
11001989.
PMID
38589369.
-
^ Wright ES (2020).
"RNAconTest: comparing tools for noncoding RNA multiple sequence alignment based on structural consistency". RNA. 26: 531–540.
doi:
10.1261/rna.073015.119.
PMC
7161358.
PMID
32005745.
-
^ Wright ES (2015).
"DECIPHER: harnessing local sequence context to improve protein multiple sequence alignment". BMC Bioinformatics. 16: 322.
doi:
10.1186/s12859-015-0749-z.
PMC
4595117.
PMID
26445311.
-
^ Noguera DR, Wright ES, Camejo P, Yilmaz LS (2014). "Mathematical tools to optimize the design of oligonucleotide probes and primers". Applied Microbiology and Biotechnology. 98 (23): 9595–608.
doi:
10.1007/s00253-014-6165-x.
PMID
25359473.
S2CID
903222.
-
^ Wright ES, Yilmaz LS, Ram S, Gasser JM, Harrington GW, Noguera DR (2014). "Exploiting extension bias in polymerase chain reaction to improve primer specificity in ensembles of nearly identical DNA templates". Environmental Microbiology. 16 (5): 1354–1365.
doi:
10.1111/1462-2920.12259.
PMID
24750536.
-
^ Wright ES, Vetsigian KH (2016).
"DesignSignatures: a tool for designing primers that yields amplicons with distinct signatures". Bioinformatics. 32 (10): 1565–1567.
doi:
10.1093/bioinformatics/btw047.
PMID
26803162.
-
^ Wright ES, Yilmaz LS, Corcoran AM, Okten HE, Noguera DR (2014).
"Automated Design of Probes for rRNA-Targeted Fluorescence In Situ Hybridization Reveals the Advantages of Using Dual Probes for Accurate Identification". Applied and Environmental Microbiology. 80 (16): 5124–5133.
doi:
10.1128/AEM.01685-14.
PMC
4135741.
PMID
24928876.
-
^ Yilmaz LS, Loy A, Wright ES, Wagner M, Noguera DR (2012).
"Modeling formamide denaturation of probe-target hybrids for improved microarray probe design in microbial diagnostics". PLOS ONE. 7 (8): e43862.
Bibcode:
2012PLoSO...743862Y.
doi:
10.1371/journal.pone.0043862.
PMC
3428302.
PMID
22952791.
-
^ Wright ES, Yilmaz LS, Noguera DR (2012).
"DECIPHER, a search-based approach to chimera identification for 16S rRNA sequences". Applied and Environmental Microbiology. 78 (3): 717–725.
doi:
10.1128/AEM.06516-11.
PMC
3264099.
PMID
22101057.
-
^ Murali A, Bhargava A, Wright ES (2018).
"IDTAXA: a novel approach for accurate taxonomic classification of microbiome sequences". Microbiome. 6 (140): 140.
doi:
10.1186/s40168-018-0521-5.
PMC
6085705.
PMID
30092815.
-
^ Cooley N, Wright ES (2021).
"Accurate annotation of protein coding sequences with IDTAXA". NAR Genomics and Bioinformatics. 3 (3): 1–10.
doi:
10.1093/nargab/lqab080.
PMC
8445202.
PMID
34541527.
-
^ Wright ES (February 2022).
"FindNonCoding: rapid and simple detection of non-coding RNAs in genomes". Bioinformatics. 38 (3): 841–843.
doi:
10.1093/bioinformatics/btab708.
PMC
10060727.
PMID
34636849.