Citations
- DECIPHER software
- Versions 3.x:
ES Wright (2024) "Fast and Flexible Search for Homologous Biological Sequences with DECIPHER v3." The R Journal, 16(2), 191-200.
- Versions 2.x:
ES Wright (2016) "Using DECIPHER v2.0 to Analyze Big Biological Sequence Data in R." The R Journal, 8(1), 352-359.
- Versions 3.x:
- Specific functions
- DetectRepeats:
Cho, S.-T. & Wright, E. S. (2025) "Accurate detection of tandem repeats exposes ubiquitous reuse of biological sequences." Nucleic Acids Research, doi:10.1093/nar/gkaf866.
- Clusterize:
ES Wright (2024) "Accurately clustering biological sequences in linear time by relatedness sorting." Nature Communications, doi:10.1038/s41467-024-47371-9.
- Find Chimeras:
ES Wright et al. (2012) "DECIPHER, A Search-Based Approach to Chimera Identification for 16S rRNA Sequences." Applied and Environmental Microbiology, doi:10.1128/AEM.06516-11.
- DetectRepeats:
- Sequence alignment
- Amino acid sequence alignment:
ES Wright (2015) "DECIPHER: harnessing local sequence context to improve protein multiple sequence alignment." BMC Bioinformatics, doi:10.1186/s12859-015-0749-z.
- DNA or RNA sequence alignment:
ES Wright (2020) "RNAconTest: Comparing Tools for Noncoding RNA Multiple Sequence Alignment Based on Structural Consistency." RNA, doi:10.1261/rna.073015.119.
- Amino acid sequence alignment:
- Classification
- IDTAXA protein (functional) classification:
NP Cooley & ES Wright (2021) "Accurate annotation of protein coding sequences with IDTAXA." NAR Genomics and Bioinformatics, doi:10.1093/nargab/lqab080.
- IDTAXA nucleotide (organismal) classification:
A Murali et al. (2018) "IDTAXA: a novel approach for accurate taxonomic classification of microbiome sequences." Microbiome, doi:10.1186/s40168-018-0521-5.
- IDTAXA protein (functional) classification:
- Oligo design
- Design Signatures:
ES Wright & KH Vetsigian (2016) "DesignSignatures: a tool for designing primers that yields amplicons with distinct signatures." Bioinformatics, doi:10.1093/bioinformatics/btw047.
- Design Primers:
ES Wright et al. (2014) "Exploiting Extension Bias in PCR to Improve Primer Specificity in Ensembles of Nearly Identical DNA Templates." Environmental Microbiology, doi:10.1111/1462-2920.12259.
- Design Probes and ProbeMelt (FISH):
ES Wright et al. (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, doi:10.1128/AEM.01685-14.
- Design Signatures: