DECIPHER (software)
| Developer(s) | Erik Wright |
|---|---|
| Stable release | 2.0.0 / 2016 |
| Written in | R and C |
| Operating system | UNIX, Linux, Mac, MS-Windows |
| Type | Bioinformatics |
| License | GNU General Public License, version 3 |
| Website |
decipher |
DECIPHER is a software toolset that can be used for deciphering and managing biological sequences efficiently using the R programming language. Some functionality of the program is accessible online through web tools.
Features
- Sequence databases: import, maintain, view, and export sequences.
- Multiple sequence alignment: align DNA, RNA, or amino acid sequences.[1]
- Genome Alignment: find and align the syntenic regions of multiple genomes.
- Oligonucleotide design:[2] primer design[3] for PCR, probe design for FISH[4] or microarrays.[5]
- Manipulate sequences: correct frameshifts, reorient nucleotides, determine consensus, or digest with restriction enzymes.
- Analyze sequences: find chimeras,[6] predict secondary structure, and create phylogenetic trees.
References
- ↑ Wright ES (2015). "DECIPHER: harnessing local sequence context to improve protein multiple sequence alignment.". BMC Bioinformatics. doi:10.1186/s12859-015-0749-z. 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. doi:10.1007/s00253-014-6165-x. PMID 25359473.
- ↑ 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 15 (5): 1354–1365. doi:10.1111/1462-2920.12259. PMID 24750536.
- ↑ 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. 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. doi:10.1371/journal.pone.0043862. 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. PMID 22101057.
External links
See also
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