# Tools for curating, analyzing, and manipulating biological sequences

## Documentation for package ‘DECIPHER’ version 3.0.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.

## Help Pages

A B C D E F G H I L M N O P R S T W misc

DECIPHER-package | Tools for curating, analyzing, and manipulating biological sequences

## -- A --

AA_REDUCED | Reduced amino acid alphabets
Add2DB | Add Data to a Database
AdjustAlignment | Improve An Existing Alignment By Adjusting Gap Placements
AlignDB | Align Two Sets of Aligned Sequences in a Sequence Database
AlignPairs | Align pairs of sequences
AlignProfiles | Align Two Sets of Aligned Sequences
AlignSeqs | Align a Set of Unaligned Sequences
AlignSynteny | Pairwise Aligns Syntenic Blocks
AlignTranslation | Align Sequences By Their Amino Acid Translation
AmplifyDNA | Simulate Amplification of DNA by PCR
Array2Matrix | Create a Matrix Representation of a Microarray

## -- B --

BLOSUM | BLOSUM Amino Acid Substitution Matrices
BrowseDB | View a Database Table in a Web Browser
BrowseSeqs | View Sequences in a Web Browser

## -- C --

c.Taxa | Taxa training and testing objects
CalculateEfficiencyArray | Predict the Hybridization Efficiency of Probe/Target Sequence Pairs
CalculateEfficiencyFISH | Predict Thermodynamic Parameters of Probe/Target Sequence Pairs
CalculateEfficiencyPCR | Predict Amplification Efficiency of Primer Sequences
Clusterize | Cluster Sequences By Distance
Codec | Compression/Decompression of Character Vectors
ConsensusSequence | Create a Consensus Sequence
Cophenetic | Compute cophenetic distances on dendrogram objects
CorrectFrameshifts | Corrects Frameshift Errors In Protein Coding Sequences
CreateChimeras | Create Artificial Chimeras

## -- D --

DB2Seqs | Export Database Sequences to a FASTA or FASTQ File
DECIPHER | Tools for curating, analyzing, and manipulating biological sequences
deltaGrules | Free Energy of Hybridization of Probe/Target Quadruplets on Microarrays
deltaGrulesRNA | Pseudoenergy Parameters for RNA Quadruplets
deltaHrules | Change in Enthalpy of Hybridization of DNA/DNA Quadruplets in Solution
deltaHrulesRNA | Change in Enthalpy of Hybridization of RNA/RNA Quadruplets in Solution
deltaSrules | Change in Entropy of Hybridization of DNA/DNA Quadruplets in Solution
deltaSrulesRNA | Change in Entropy of Hybridization of RNA/RNA Quadruplets in Solution
DesignArray | Design a Set of DNA Microarray Probes for Detecting Sequences
DesignPrimers | Design PCR Primers Targeting a Specific Group of Sequences
DesignProbes | Design FISH Probes Targeting a Specific Group of Sequences
DesignSignatures | Design PCR Primers for Amplifying Group-Specific Signatures
DetectRepeats | Detect Repeats in a Sequence
DigestDNA | Simulate Restriction Digestion of DNA
Disambiguate | Expand Ambiguities into All Permutations of a DNAStringSet
DistanceMatrix | Calculate the Distances Between Sequences

## -- E --

ExtractGenes | Extract Predicted Genes from a Genome

## -- F --

FindChimeras | Find Chimeras in a Sequence Database
FindGenes | Find Genes in a Genome
FindNonCoding | Find Non-Coding RNAs in a Genome
FindSynteny | Finds Synteny in a Sequence Database
FormGroups | Forms Groups By Rank

## -- G --

Genes-class | Genes objects and accessors

## -- H --

HEC_MI1 | Mutual Information for Protein Secondary Structure Prediction
HEC_MI2 | Mutual Information for Protein Secondary Structure Prediction

## -- I --

IdConsensus | Create Consensus Sequences by Groups
IdentifyByRank | Identify By Taxonomic Rank
IdLengths | Determine the Number of Characters in Each Sequence
IdTaxa | Assign Sequences a Taxonomic Classification
IndexSeqs | Build an inverted index
InvertedIndex-class | InvertedIndex objects

## -- L --

LearnNonCoding | Learn a Non-Coding RNA Model
LearnTaxa | Train a Classifier for Assigning Taxonomy

## -- M --

MapCharacters | Map Changes in Ancestral Character States
MaskAlignment | Mask Highly Variable Regions of An Alignment
MeltDNA | Simulate Melting of DNA
MIQS | MIQS Amino Acid Substitution Matrix
MMLSUM | MMLSUM Amino Acid Substitution Matrices
MODELS | Available Models of Sequence Evolution

## -- N --

NNLS | Sequential Coordinate-wise Algorithm for the Non-negative Least Squares Problem
NonCoding-class | NonCoding Objects and Methods
NonCodingRNA_Archaea | NonCoding Models for Common Non-Coding RNA Families
NonCodingRNA_Bacteria | NonCoding Models for Common Non-Coding RNA Families
NonCodingRNA_Eukarya | NonCoding Models for Common Non-Coding RNA Families

## -- O --

OrientNucleotides | Orient Nucleotide Sequences

## -- P --

pairs.Synteny | Synteny blocks and hits
PAM | PAM Amino Acid Substitution Matrices
PFASUM | PFASUM Amino Acid Substitution Matrices
plot.Genes | Genes objects and accessors
plot.Synteny | Synteny blocks and hits
plot.Taxa | Taxa training and testing objects
PredictDBN | Predict RNA Secondary Structure in Dot-Bracket Notation
PredictHEC | Predict Protein Secondary Structure as Helix, Beta-Sheet, or Coil
print.Genes | Genes objects and accessors
print.InvertedIndex | InvertedIndex objects
print.NonCoding | NonCoding Objects and Methods
print.Synteny | Synteny blocks and hits
print.Taxa | Taxa training and testing objects

## -- R --

ReadDendrogram | Read a Dendrogram from a Newick Formatted File
RemoveGaps | Remove Gap Characters in Sequences
RESTRICTION_ENZYMES | Common Restriction Enzyme's Cut Sites

## -- S --

ScoreAlignment | Score a Multiple Sequence Alignment
SearchDB | Obtain Specific Sequences from a Database
SearchIndex | Search an inverted index
Seqs2DB | Add Sequences from Text File to Database
StaggerAlignment | Produce a Staggered Alignment
Synteny-class | Synteny blocks and hits

## -- T --

Taxa-class | Taxa training and testing objects
TerminalChar | Determine the Number of Terminal Characters
TileSeqs | Form a Set of Tiles for Each Group of Sequences.
TrainingSet_16S | Training Set for Classification of 16S rRNA Gene Sequences
TreeLine | Construct a Phylogenetic Tree
TrimDNA | Trims DNA Sequences to the High Quality Region Between Patterns

## -- W --

WriteDendrogram | Write a Dendrogram to Newick Format
WriteGenes | Write Genes to a File

## -- misc --

[.Genes | Genes objects and accessors
[.Synteny | Synteny blocks and hits
[.Taxa | Taxa training and testing objects