DECIPHER (software)

DECIPHER
DECIPHER
Developer(s)	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.codes

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.^[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.

References

^ Wright ES (2024). "Accurately clustering biological sequences in linear time by relatedness sorting". Nature Communications. 15 (1): 3047. Bibcode:2024NatCo..15.3047W. 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 (5): 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. Bibcode:2014EnvMi..16.1354W. 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. Bibcode:2014ApEnM..80.5124W. 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.{{cite journal}}: CS1 maint: article number as page number (link)
^ 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. Bibcode:2012ApEnM..78..717W. 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.

External links

Official website

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[Wright2024-1] Wright ES (2024). "Accurately clustering biological sequences in linear time by relatedness sorting". Nature Communications. 15 (1): 3047. Bibcode:2024NatCo..15.3047W. doi:10.1038/s41467-024-47371-9. PMC 11001989. PMID 38589369.

[Wright2020-2] Wright ES (2020). "RNAconTest: comparing tools for noncoding RNA multiple sequence alignment based on structural consistency". RNA. 26 (5): 531–540. doi:10.1261/rna.073015.119. PMC 7161358. PMID 32005745.

[Wright2015-3] 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.

[Noguera2014-4] 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.

[Wright2014a-5] 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. Bibcode:2014EnvMi..16.1354W. doi:10.1111/1462-2920.12259. PMID 24750536.

[Wright2016-6] 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.

[Wright2014b-7] 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. Bibcode:2014ApEnM..80.5124W. doi:10.1128/AEM.01685-14. PMC 4135741. PMID 24928876.

[Yilmaz2012-8] 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.{{cite journal}}: CS1 maint: article number as page number (link)

[Wright2012-9] 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. Bibcode:2012ApEnM..78..717W. doi:10.1128/AEM.06516-11. PMC 3264099. PMID 22101057.

[Murali2018-10] 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.

[Cooley2021-11] 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.

[pmid34636849-12] 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.

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