DECIPHER (software)
DECIPHER is a software toolset that can be used to decipher and manage biological sequences efficiently using the programming language R. Some functions of the program are accessible online through web tools.
| Developer(s) | Erik Wright |
|---|---|
| Stable release | 2.18.1
/ 2020 |
| Written in | R, C |
| Operating system | Unix, Linux, macOS, Windows |
| Platform | IA-32, x86-64 |
| Available in | English |
| Type | Bioinformatics |
| License | GPL 3 |
| Website | decipher |
Features
- Sequence databases: import, maintain, view, and export sequences.
- Multiple sequence alignment: align sequences of DNA, RNA, or amino acids.[1]
- Genome alignment: find and align the syntenic regions of multiple genomes.
- Oligonucleotide design:[2] primer design[3][4] for polymerase chain reaction (PCR), probe design for fluorescence in situ hybridization (FISH)[5] or DNA microarrays.[6]
- Manipulate sequences: trim low quality regions, correct frameshifts, reorient nucleotides, determine consensus, or digest with restriction enzymes.
- Analyze sequences: find chimeras,[7] predict secondary structure, classify into a taxonomy,[8] create phylogenetic trees, and ancestral reconstruction.
- Gene finding: predict genes in a genome, extract them from the genome, and export them to a file.
See also
References
- 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.
- 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.
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