Software:DECIPHER
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| Developer(s) | Erik Wright |
|---|---|
| Stable release | 2.20.0
/ 2021 |
| 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 |
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.
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 of organisms or functions,[8] create phylogenetic trees, and ancestral reconstruction.
- Gene finding: predict coding and non-coding genes[9] in a genome, extract them from the genome, and export them to a file.
See also
- Sequence alignment software
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. PMID 26445311.
- ↑ "Mathematical tools to optimize the design of oligonucleotide probes and primers". Applied Microbiology and Biotechnology 98 (23): 9595–608. 2014. doi:10.1007/s00253-014-6165-x. PMID 25359473.
- ↑ "Exploiting extension bias in polymerase chain reaction to improve primer specificity in ensembles of nearly identical DNA templates". Environmental Microbiology 16 (5): 1354–1365. 2014. doi:10.1111/1462-2920.12259. PMID 24750536.
- ↑ "DesignSignatures: a tool for designing primers that yields amplicons with distinct signatures". Bioinformatics 32 (10): 1565–1567. 2016. doi:10.1093/bioinformatics/btw047. PMID 26803162.
- ↑ "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. 2014. doi:10.1128/AEM.01685-14. PMID 24928876.
- ↑ "Modeling formamide denaturation of probe-target hybrids for improved microarray probe design in microbial diagnostics". PLOS ONE 7 (8): e43862. 2012. doi:10.1371/journal.pone.0043862. PMID 22952791. Bibcode: 2012PLoSO...743862Y.
- ↑ "DECIPHER, a search-based approach to chimera identification for 16S rRNA sequences". Applied and Environmental Microbiology 78 (3): 717–725. 2012. doi:10.1128/AEM.06516-11. PMID 22101057.
- ↑ "IDTAXA: a novel approach for accurate taxonomic classification of microbiome sequences". Microbiome 6 (140): 140. 2018. doi:10.1186/s40168-018-0521-5. PMID 30092815.
- ↑ "FindNonCoding: rapid and simple detection of non-coding RNAs in genomes.". Bioinformatics Oct12: btab708. 2021. doi:10.1093/bioinformatics/btab708. PMID 34636849.
External links
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