SequenceAnalysis: Sequence Analysis

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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.

Author
Babak Khorsand [aut, cre], Javad Zahiri [ths], Abdorreza Savadi [ths]
Date of publication
2016-08-15 16:28:52
Maintainer
Babak Khorsand <khorsand@yahoo.com>
License
GPL
Version
1.3

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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

Files in this package

SequenceAnalysis
SequenceAnalysis/NAMESPACE
SequenceAnalysis/R
SequenceAnalysis/R/GetProteinOrganism.R
SequenceAnalysis/R/Reverse.R
SequenceAnalysis/R/GetNuclotideSequence.R
SequenceAnalysis/R/ReverseComplement.R
SequenceAnalysis/R/GetLocalization.R
SequenceAnalysis/R/GC.R
SequenceAnalysis/R/sysdata.rda
SequenceAnalysis/R/CodonUsage.R
SequenceAnalysis/R/StackingEnergy.R
SequenceAnalysis/R/AminoAcidToCodon.R
SequenceAnalysis/R/CodonToAminoAcid.R
SequenceAnalysis/R/Complement.R
SequenceAnalysis/R/GetProteinSequence.R
SequenceAnalysis/R/AAC.R
SequenceAnalysis/MD5
SequenceAnalysis/DESCRIPTION
SequenceAnalysis/man
SequenceAnalysis/man/SequenceAnalysis.Reverse.Rd
SequenceAnalysis/man/SequenceAnalysis.Complement.Rd
SequenceAnalysis/man/SequenceAnalysis.AAC.Rd
SequenceAnalysis/man/SequenceAnalysis.GetLocalization.Rd
SequenceAnalysis/man/SequenceAnalysis.ReverseComplement.Rd
SequenceAnalysis/man/SequenceAnalysis.GC.Rd
SequenceAnalysis/man/SequenceAnalysis.CodonToAminoAcid.Rd
SequenceAnalysis/man/SequenceAnalysis.GetProteinSequence.Rd
SequenceAnalysis/man/SequenceAnalysis.GetNucleotideSequence.Rd
SequenceAnalysis/man/SequenceAnalysis.CodonUsage.Rd
SequenceAnalysis/man/SequenceAnalysis.AminoAcidToCodon.Rd
SequenceAnalysis/man/SequenceAnalysis.GetProteinOrganism.Rd
SequenceAnalysis/man/SequenceAnalysis.StackingEnergy.Rd