DECIPHER (software)

• 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.{{cite journal |author=Wright ES |title=Accurately clustering biological sequences in linear time by relatedness sorting |journal=Nature Communications |year=2024 |pmid= 38589369 |doi=10.1038/s41467-024-47371-9 |volume=15 |issue=1 |pmc=11001989 |pages=3047 |doi-access=free |bibcode=2024NatCo..15.3047W }}
• Multiple sequence alignment: align sequences of DNA, RNA,{{cite journal |author=Wright ES |title=RNAconTest: comparing tools for noncoding RNA multiple sequence alignment based on structural consistency |journal=RNA |year=2020 |pmid=32005745 |doi=10.1261/rna.073015.119 |volume=26 |issue=5 |pmc=7161358 |pages=531–540 |doi-access=free }} or amino acids.{{cite journal |author=Wright ES |title=DECIPHER: harnessing local sequence context to improve protein multiple sequence alignment |journal=BMC Bioinformatics |year=2015 |pmid=26445311 |doi=10.1186/s12859-015-0749-z |volume=16 |pmc=4595117 |pages=322 |doi-access=free }}
• Genome alignment: find and align the syntenic regions of multiple genomes.
• Oligonucleotide design:{{cite journal |vauthors=Noguera DR, Wright ES, Camejo P, Yilmaz LS |title=Mathematical tools to optimize the design of oligonucleotide probes and primers |journal=Applied Microbiology and Biotechnology |year=2014 |pmid=25359473 |doi=10.1007/s00253-014-6165-x |volume=98 |issue=23 |pages=9595–608|s2cid=903222 }} primer design{{cite journal |vauthors=Wright ES, Yilmaz LS, Ram S, Gasser JM, Harrington GW, Noguera DR |title=Exploiting extension bias in polymerase chain reaction to improve primer specificity in ensembles of nearly identical DNA templates |journal=Environmental Microbiology |volume= 16|issue=5 |pages=1354–1365 |year=2014 |pmid=24750536 |doi=10.1111/1462-2920.12259|bibcode=2014EnvMi..16.1354W }}{{cite journal |vauthors=Wright ES, Vetsigian KH |title=DesignSignatures: a tool for designing primers that yields amplicons with distinct signatures |journal=Bioinformatics |volume=32 |issue=10 |pages=1565–1567 |year=2016 |pmid=26803162 |doi=10.1093/bioinformatics/btw047|doi-access=free }} for polymerase chain reaction (PCR), probe design for fluorescence in situ hybridization (FISH){{cite journal |vauthors=Wright ES, Yilmaz LS, Corcoran AM, Okten HE, Noguera DR |title=Automated Design of Probes for rRNA-Targeted Fluorescence In Situ Hybridization Reveals the Advantages of Using Dual Probes for Accurate Identification |journal=Applied and Environmental Microbiology |volume=80 |issue=16 |pages=5124–5133 |year=2014 |pmid=24928876 |doi=10.1128/AEM.01685-14 |pmc=4135741|bibcode=2014ApEnM..80.5124W }} or DNA microarrays.{{cite journal |vauthors=Yilmaz LS, Loy A, Wright ES, Wagner M, Noguera DR |title=Modeling formamide denaturation of probe-target hybrids for improved microarray probe design in microbial diagnostics |journal=PLOS ONE |year=2012 |pmid=22952791 |doi=10.1371/journal.pone.0043862 |volume=7 |issue=8 |pmc=3428302 |bibcode=2012PLoSO...743862Y |pages=e43862|doi-access=free }}
• Manipulate sequences: trim low quality regions, correct frameshifts, reorient nucleotides, determine consensus, or digest with restriction enzymes.
• Analyze sequences: find chimeras,{{cite journal |vauthors=Wright ES, Yilmaz LS, Noguera DR |title=DECIPHER, a search-based approach to chimera identification for 16S rRNA sequences |journal=Applied and Environmental Microbiology |volume=78 |issue=3 |pages=717–725 |year=2012 |pmid=22101057 |doi=10.1128/AEM.06516-11 |pmc=3264099|bibcode=2012ApEnM..78..717W }} detect repeats, predict secondary structure, classify into a taxonomy of organisms{{cite journal |vauthors=Murali A, Bhargava A, Wright ES |title=IDTAXA: a novel approach for accurate taxonomic classification of microbiome sequences |journal=Microbiome |volume=6 |issue=140 |pages=140 |year=2018 |doi=10.1186/s40168-018-0521-5|pmid=30092815 |pmc=6085705 |doi-access=free }} or functions,{{cite journal |vauthors=Cooley N, Wright ES |title=Accurate annotation of protein coding sequences with IDTAXA |journal=NAR Genomics and Bioinformatics |volume=3 |issue=3 |pages=1–10 |year=2021 |doi=10.1093/nargab/lqab080 |pmid=34541527 |pmc=8445202 |doi-access=free}} create phylogenetic trees, and ancestral reconstruction.
• Gene finding: predict coding and non-coding genes{{cite journal |vauthors=Wright ES |date=February 2022 |title=FindNonCoding: rapid and simple detection of non-coding RNAs in genomes. |journal=Bioinformatics |volume=38 |issue=3|pages=841–843 |pmid=34636849 |pmc=10060727 |doi=10.1093/bioinformatics/btab708 |doi-access=free}} in a genome, extract them from the genome, and export them to a file.

{{Div col|colwidth=22em}}

• Sequence alignment software

{{div col end}}

{{Reflist|30em}}

• {{Official website|decipher.codes}}

Category:Phylogenetics software

{{science-software-stub}}