DECIPHER (software)

DECIPHER
Developer(s)	Erik Wright
Stable release	3.4.0 / 2025 (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.

See also

• Sequence alignment software

References

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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.

External links

• Official website