DECIPHER (software) explained

DECIPHER
Developer:	Erik Wright
Latest Release Version:	3.2.0
Programming Language:	R, C
Operating System:	Unix, Linux, macOS, Windows
Platform:	x86-64, ARM
Language:	English
Genre:	Bioinformatics
License:	GPL 3

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

Notes and References

1. Wright ES . Accurately clustering biological sequences in linear time by relatedness sorting . Nature Communications . 2024 . 38589369 . 10.1038/s41467-024-47371-9 . 15 . 11001989 . 3047 . free .
2. Wright ES . RNAconTest: comparing tools for noncoding RNA multiple sequence alignment based on structural consistency . RNA . 2020 . 32005745 . 10.1261/rna.073015.119 . 26 . 7161358 . 531-540 . free .
3. Wright ES . DECIPHER: harnessing local sequence context to improve protein multiple sequence alignment . BMC Bioinformatics . 2015 . 26445311 . 10.1186/s12859-015-0749-z . 16 . 4595117 . 322 . free .
4. Noguera DR, Wright ES, Camejo P, Yilmaz LS . Mathematical tools to optimize the design of oligonucleotide probes and primers . Applied Microbiology and Biotechnology . 2014 . 25359473 . 10.1007/s00253-014-6165-x . 98 . 23 . 9595–608. 903222 .
5. Wright ES, Yilmaz LS, Ram S, Gasser JM, Harrington GW, Noguera DR . 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 . 24750536 . 10.1111/1462-2920.12259.
6. Wright ES, Vetsigian KH . DesignSignatures: a tool for designing primers that yields amplicons with distinct signatures . Bioinformatics . 32 . 10 . 1565–1567 . 2016 . 26803162 . 10.1093/bioinformatics/btw047. free .
7. Wright ES, Yilmaz LS, Corcoran AM, Okten HE, Noguera DR . 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 . 24928876 . 10.1128/AEM.01685-14 . 4135741.
8. Yilmaz LS, Loy A, Wright ES, Wagner M, Noguera DR . Modeling formamide denaturation of probe-target hybrids for improved microarray probe design in microbial diagnostics . PLOS ONE . 2012 . 22952791 . 10.1371/journal.pone.0043862 . 7 . 8 . 3428302 . 2012PLoSO...743862Y . e43862. free .
9. Wright ES, Yilmaz LS, Noguera DR . DECIPHER, a search-based approach to chimera identification for 16S rRNA sequences . Applied and Environmental Microbiology . 78 . 3 . 717–725 . 2012 . 22101057 . 10.1128/AEM.06516-11 . 3264099.
10. Murali A, Bhargava A, Wright ES . IDTAXA: a novel approach for accurate taxonomic classification of microbiome sequences . Microbiome . 6 . 140 . 140 . 2018 . 10.1186/s40168-018-0521-5. 30092815 . 6085705 . free .
11. Cooley N, Wright ES . Accurate annotation of protein coding sequences with IDTAXA . NAR Genomics and Bioinformatics . 3 . 3 . 1-10 . 2021 . 10.1093/nargab/lqab080 . 34541527 . 8445202 . free.
12. Wright ES . February 2022 . FindNonCoding: rapid and simple detection of non-coding RNAs in genomes. . Bioinformatics . 38 . 3. 841–843 . 34636849 . 10060727 . 10.1093/bioinformatics/btab708 . free.