SequenceAnalysis: Sequence Analysis
Version 1.3

Provides: 1) By Giving UniProtKB, the Protein Sequence will be returned from UniProt database. 2)By Giving UniProtKB, the Nucleotide Sequence will be returned from EBI database. 3) Amino acid Composition is calculated by four different methods: a) Twenty-two independent categories are considered, with one amino acid for each category. B) Five categories (Nonpolar Aliphatic, Nonpolar Aromatic, Polar Uncharged, Polar Positively Charged, Polar Negatively Charged) are considered according to the standard chemical structures of amino acids. c) Six categories (Nonpolar Aliphatic, Nonpolar Aromatic, Polar Uncharged, Polar Positively Charged, Polar Negatively Charged, Special cases) are considered which Cysteine, Selenocysteine, Glycine and Proline are placed in Special cases group. d)Eight categories are clustered via k-means algorithm on Physicochemical index of amino acids. 4) GC Content: Percentage of nucleotide g and c in sequence. 5) Codon usage: Frequency of occurrence of synonymous codons. 6) Stacking Energy: The NN model for nucleic acids assumes that the stability of a given base pair depends on the identity and orientation of neighboring base pairs. Stacking Energy = DeltaG(total) = Sigma (n(i)*DeltaG(i)) + DeltaG(init) + DeltaG(end) + DeltaG(sym), which DeltaG for i, init and end is obtained by Unified NN free energy parameter. Symmetry of self-complementary duplexes is also included by DeltaG(sym) equals to +0.43 (kcal/mol) if the duplex is self-complementary and zero if it is non-self-complementary. 7) Complement of desired nucleotide sequence. 8) Reverse of desired nucleotide sequence. 9) Reverse-Complement of desired nucleotide sequence. 10) Protein, Gene and Organism of desired UniProt ID. 11) Converting nucleotide sequence to protein sequence. 12) Getting Localization From Gene Ontology Cellular Component inside Uniprot. 13) All related codons of desired amino acid.

Browse man pages Browse package API and functions Browse package files

AuthorBabak Khorsand [aut, cre], Javad Zahiri [ths], Abdorreza Savadi [ths]
Date of publication2016-08-15 16:28:52
MaintainerBabak Khorsand <khorsand@yahoo.com>
LicenseGPL
Version1.3
Package repositoryView on CRAN
InstallationInstall the latest version of this package by entering the following in R:
install.packages("SequenceAnalysis")

Man pages

SequenceAnalysis.AAC: SequenceAnalysis.AAC
SequenceAnalysis.AminoAcidToCodon: SequenceAnalysis.AminoAcidToCodon
SequenceAnalysis.CodonToAminoAcid: SequenceAnalysis.CodonToAminoAcid
SequenceAnalysis.CodonUsage: SequenceAnalysis.CodonUsage
SequenceAnalysis.Complement: SequenceAnalysis.Complement
SequenceAnalysis.GC: SequenceAnalysis.GC
SequenceAnalysis.GetLocalization: SequenceAnalysis.GetLocalization
SequenceAnalysis.GetNucleotideSequence: SequenceAnalysis.GetNucleotideSequence
SequenceAnalysis.GetProteinOrganism: SequenceAnalysis.GetProteinOrganism
SequenceAnalysis.GetProteinSequence: SequenceAnalysis.GetProteinSequence
SequenceAnalysis.Reverse: SequenceAnalysis.Reverse
SequenceAnalysis.ReverseComplement: SequenceAnalysis.ReverseComplement
SequenceAnalysis.StackingEnergy: SequenceAnalysis.StackingEnergy

Functions

SequenceAnalysis.AAC Man page Source code
SequenceAnalysis.AminoAcidToCodon Man page Source code
SequenceAnalysis.CodonToAminoAcid Man page Source code
SequenceAnalysis.CodonUsage Man page Source code
SequenceAnalysis.Complement Man page Source code
SequenceAnalysis.GC Man page Source code
SequenceAnalysis.GetLocalization Man page Source code
SequenceAnalysis.GetNucleotideSequence Man page Source code
SequenceAnalysis.GetProteinOrganism Man page Source code
SequenceAnalysis.GetProteinSequence Man page Source code
SequenceAnalysis.Reverse Man page Source code
SequenceAnalysis.ReverseComplement Man page Source code
SequenceAnalysis.StackingEnergy Man page Source code

Files

NAMESPACE
R
R/GetProteinOrganism.R
R/Reverse.R
R/GetNuclotideSequence.R
R/ReverseComplement.R
R/GetLocalization.R
R/GC.R
R/sysdata.rda
R/CodonUsage.R
R/StackingEnergy.R
R/AminoAcidToCodon.R
R/CodonToAminoAcid.R
R/Complement.R
R/GetProteinSequence.R
R/AAC.R
MD5
DESCRIPTION
man
man/SequenceAnalysis.Reverse.Rd
man/SequenceAnalysis.Complement.Rd
man/SequenceAnalysis.AAC.Rd
man/SequenceAnalysis.GetLocalization.Rd
man/SequenceAnalysis.ReverseComplement.Rd
man/SequenceAnalysis.GC.Rd
man/SequenceAnalysis.CodonToAminoAcid.Rd
man/SequenceAnalysis.GetProteinSequence.Rd
man/SequenceAnalysis.GetNucleotideSequence.Rd
man/SequenceAnalysis.CodonUsage.Rd
man/SequenceAnalysis.AminoAcidToCodon.Rd
man/SequenceAnalysis.GetProteinOrganism.Rd
man/SequenceAnalysis.StackingEnergy.Rd
SequenceAnalysis documentation built on May 20, 2017, 5:41 a.m.