Learn R Programming

DECIPHER (version 2.0.2)

Tools for curating, analyzing, and manipulating biological sequences

Description

A toolset for deciphering and managing biological sequences.

Copy Link

Version

Version

2.0.2

License

GPL-3

Maintainer

Erik Wright

Last Published

February 15th, 2017

Functions in DECIPHER (2.0.2)

CalculateEfficiencyPCR

Predict Amplification Efficiency of Primer Sequences
AdjustAlignment

Improve An Existing Alignment By Adjusting Gap Placements
MaskAlignment

Mask Highly Variable Regions of An Alignment
AlignSeqs

Align a Set of Unaligned Sequences
DesignSignatures

Design PCR Primers for Amplifying Group-Specific Signatures
DistanceMatrix

Calculate the Distances Between Sequences
SearchDB

Obtain Specific Sequences from a Database
IdConsensus

Create Consensus Sequences by Groups
WriteDendrogram

Write a Dendrogram to Newick Format
TileSeqs

Form a Set of Tiles for Each Group of Sequences.
Seqs2DB

Add Sequences from Text File to Database
AlignProfiles

Align Two Sets of Aligned Sequences
BrowseSeqs

View Sequences in a Web Browser
CalculateEfficiencyFISH

Predict Thermodynamic Parameters of Probe/Target Sequence Pairs
Array2Matrix

Create a Matrix Representation of a Microarray
DesignPrimers

Design PCR Primers Targeting a Specific Group of Sequences
DB2Seqs

Export Database Sequences to a FASTA or FASTQ File
MIQS

MIQS Amino Acid Substitution Matrix
CalculateEfficiencyArray

Predict the Hybridization Efficiency of Probe/Target Sequence Pairs
BrowseDB

View a Database Table in a Web Browser
DesignProbes

Design FISH Probes Targeting a Specific Group of Sequences
FormGroups

Forms Groups By Rank
IdentifyByRank

Identify By Taxonomic Rank
DECIPHER-package

Tools for curating, analyzing, and manipulating biological sequences
MODELS

Available Models of DNA Evolution
AlignDB

Align Two Sets of Aligned Sequences in a Sequence Database
OrientNucleotides

Orient nucleotide sequences
MeltDNA

Simulate Melting of DNA
deltaGrules

Free Energy of Hybridization of Probe/Target Quadruplets on Microarrays
deltaHrules

Change in Enthalpy of Hybridization of Primer/Target Quadruplets in Solution
CreateChimeras

Create Artificial Chimeras
CorrectFrameshifts

Corrects Frameshift Errors In Protein Coding Sequences
AlignSynteny

Pairwise Aligns Syntenic Blocks
AlignTranslation

Align Sequences By Their Amino Acid Translation
Codec

Compression/Decompression of Character Vectors
IdLengths

Determine the Number of Bases, Nonbases, and Width of Each Sequence
Disambiguate

Expand Ambiguities into All Permutations of a DNAStringSet
FindChimeras

Find Chimeras in a Sequence Database
HEC_MI

Mutual Information for Protein Secondary Structure Prediction
RESTRICTION_ENZYMES

Common Restriction Enzyme's Cut Sites
DigestDNA

Simulate Restriction Digestion of DNA
Add2DB

Add Data to a Database
AmplifyDNA

Simulate Amplification of DNA by PCR
deltaSrules

Change in Entropy of Hybridization of Primer/Target Quadruplets in Solution
ReadDendrogram

Read a Dendrogram from a Newick Formatted File
NNLS

Sequential Coordinate-wise Algorithm for the Non-negative Least Squares Problem
Synteny

Synteny blocks and hits
ConsensusSequence

Create a Consensus Sequence
DesignArray

Design a set of DNA Microarray Probes for Detecting Sequences
TerminalChar

Determine the Number of Terminal Characters
StaggerAlignment

Produce a Staggered Alignment
FindSynteny

Finds Synteny in a Sequence Database
IdClusters

Cluster Sequences By Distance or Sequence
PredictHEC

Predict Protein Secondary Structure