Feature Extraction from Biological Sequences
Amino Acid To Binary (AA2Binary)
Amino Acid Index (AAindex)
Amino Acid to K Part Composition (AAKpartComposition)
Amino Acid Autocorrelation-Autocovariance (AAutoCor)
Learn from alignments (AESNN3)
AlphabetCheck
Accumulated Nucleotide Frequency (ANF_DNA)
Accumulated riboNucleotide Frequency (ANF_RNA)
Amphiphilic Pseudo-Amino Acid Composition(series) (APAAC)
Amphiphilic Pseudo-k Nucleotide Composition-di(series) (APkNUCdi_DNA)
Amphiphilic Pseudo-k riboNucleotide Composition-di(series) (APkNUCdi_R...
Amphiphilic Pseudo-k Nucleotide Composition-Tri(series) (APkNUCTri_DNA...
Accessible Solvent Accessibility (ASA)
Adaptive skip dipeptide composition (ASDC)
Adaptive skip dinucleotide composition_DNA) (ASDC_DNA)
Adaptive skip di-ribonucleotide composition) (ASDC_RNA)
Di Nucleotide Autocorrelation-Autocovariance (AutoCorDiNUC_DNA)
Di riboNucleotide Autocorrelation-Autocovariance (AutoCorDiNUC_RNA)
Tri Nucleotide Autocorrelation-Autocovariance (AutoCorTriNUC_DNA)
Binary - 3bit - Type1 (binary_3bit_T1)
Binary - 3bit - Type2 (binary_3bit_T2)
Binary - 3bit - Type3 (binary_3bit_T3)
Binary - 3bit - Type4 (binary_3bit_T4)
Binary - 3bit - Type5 (binary_3bit_T5)
Binary - 3bit - Type6 (binary_3bit_T6)
Binary - 3bit - Type7 (binary_3bit_T7)
Binary - 5bit - Type1 (binary_5bit_T1)
Binary - 5bit - Type2 (binary_5bit_T2)
Binary - 6bit (binary_6bit)
Blosum62 (BLOSUM62)
Composition of k-Spaced Amino Acids pairs (CkSAApair)
Composition of k-Spaced Grouped Amino Acids pairs (CkSGAApair)
Composition of k-Spaced Nucleotides Pairs (CkSNUCpair_DNA)
Composition of k-Spaced riboNucleotides Pairs (CkSNUCpair_RNA)
Codon Adaption Index (codonAdaptionIndex)
Codon Fraction (CodonFraction)
Codon Usage in DNA (CodonUsage_DNA)
Codon Usage in RNA (CodonUsage_RNA)
Conjoint Triad (conjointTriad)
k-Spaced Conjoint Triad (conjointTriadKS)
Composition_Transition_Distribution (CTD)
CTD Composition (CTDC)
CTD Distribution (CTDD)
CTD Transition (CTDT)
Dipeptide Deviation from Expected Mean value (DDE)
Dinucleotide To Binary DNA (DiNUC2Binary_DNA)
Di riboNucleotide To Binary RNA (DiNUC2Binary_RNA)
Di Nucleotide Index (DiNUCindex_DNA)
Di riboNucleotide Index (DiNUCindex_RNA)
disorder Binary (DisorderB)
disorder Content (DisorderC)
disorder Simple (DisorderS)
PseAAC of distance-pairs and reduced alphabet (DistancePair)
Dinucleotide physicochemical properties (DPCP_DNA)
Di-ribonucleotide physicochemical properties (DPCP_RNA)
Enhanced Amino Acid Composition (EAAComposition)
Effective Number of Codon (EffectiveNumberCodon)
Enhanced Grouped Amino Acid Composition (EGAAComposition)
Electron-Ion Interaction Pseudopotentials (EIIP)
Enhanced Nucleotide Composition (ENUComposition_DNA)
Enhanced riboNucleotide Composition (ENUComposition_RNA)
Expected Value for K-mer Nucleotide (ExpectedValKmerNUC_DNA)
Expected Value for K-mer riboNucleotide (ExpectedValKmerNUC_RNA)
Expected Value for each Amino Acid (ExpectedValueAA)
Expected Value for Grouped Amino Acid (ExpectedValueGAA)
Expected Value for Grouped K-mer Amino Acid(ExpectedValueGKmerAA)
Expected Value for K-mer Amino Acid (ExpectedValueKmerAA)
Fasta File Reader (fa.read)
Fickett Score (fickettScore)
G_C content in DNA (G_Ccontent_DNA)
G_C content in RNA (G_Ccontent_RNA)
Grouped Amino Acid K Part Composition (GAAKpartComposition)
Group Dipeptide Deviation from Expected Mean (GrpDDE)
k Amino Acid Composition (kAAComposition)
k Grouped Amino Acid Composition (kGAAComposition)
K-Nearest Neighbor_DNA (KNN_DNA)
K-Nearest Neighbor_RNA (KNN_RNA)
K-Nearest Neighbor for Peptides (KNNPeptide)
K-Nearest Neighbor for Protein (KNNProtein)
k Nucleotide Composition (kNUComposition_DNA)
k riboNucleotide Composition (kNUComposition_RNA)
Local Position Specific k Amino Acids Frequency (LocalPoSpKAAF)
Local Position Specific k Nucleotide Frequency (LocalPoSpKNUCF_DNA)
Local Position Specific k riboNucleotide Frequency (LocalPoSpKNUCF_RNA...
Maximum Open Reading Frame in DNA (maxORF)
Maximum Open Reading Frame in RNA (maxORF_RNA)
Maximum Open Reading Frame length in DNA (maxORFlength_DNA)
Maximum Open Reading Frame length in RNA (maxORFlength_RNA)
Mismatch_DNA (Mismatch_DNA)
Mismatch_RNA (Mismatch_RNA)
Multivariate Mutual Information_DNA (MMI_DNA)
Multivariate Mutual Information_RNA (MMI_RNA)
naming Kmer (nameKmer)
Nucleotide Chemical Property (NCP_DNA)
riboNucleotide Chemical Property (NCP_RNA)
Needleman-Wunsch (needleman)
nonStandard sequence (nonStandardSeq)
Nucleotide To Binary (NUC2Binary_DNA)
riboNucleotide To Binary (NUC2Binary_RNA)
Nucleotide to K Part Composition (NUCKpartComposition_DNA)
riboNucleotide to K Part Composition (NUCKpartComposition_RNA)
Overlapping Property Features_10bit (OPF_10bit)
Overlapping property features_7bit_T1 (OPF_7bit_T1)
Overlapping property features_7bit_T2 (OPF_7bit_T2)
Overlapping property features_7bit_T3 (OPF_7bit_T3)
Parallel Correlation Pseudo Dinucleotide Composition (PCPseDNC)
Position-specific of two nucleotide_DNA (PS2_DNA)
Position-specific of two nucleotide_RNA (PS2_RNA)
Position-specific of three nucleotide_DNA (PS3_DNA)
Position-specific of three ribonucleotide_RNA (PS3_RNA)
Position-specific of four nucleotide_DNA (PS4_DNA)
Position-specific of four ribonucleotide (PS4_RNA)
Pseudo-Amino Acid Composition (Parallel) (PSEAAC)
Pseudo Electron-Ion Interaction Pseudopotentials of Trinucleotide (Pse...
Pseudo k Nucleotide Composition-Di(Parallel) (PSEkNUCdi_DNA)
Pseudo k riboNucleotide Composition-Di(Parallel) (PSEkNUCdi_RNA)
Pseudo k Nucleotide Composition-Tri(Parallel) (PSEkNUCTri_RNA)
Pseudo K_tuple Reduced Amino Acid Composition Type-1 (PseKRAAC_T1)
Pseudo K_tuple Reduced Amino Acid Composition Type-10 (PseKRAAC_T10)
Pseudo K_tuple Reduced Amino Acid Composition Type-11 (PseKRAAC_T11)
Pseudo K_tuple Reduced Amino Acid Composition Type-12 (PseKRAAC_T12)
Pseudo K_tuple Reduced Amino Acid Composition Type_13 (PseKRAAC_T13)
Pseudo K_tuple Reduced Amino Acid Composition Type-14 (PseKRAAC_T14)
Pseudo K_tuple Reduced Amino Acid Composition Type-15 (PseKRAAC_T15)
Pseudo K_tuple Reduced Amino Acid Composition Type-16 (PseKRAAC_T16)
Pseudo K_tuple Reduced Amino Acid Composition Type-2 (PseKRAAC_T2)
Pseudo K_tuple Reduced Amino Acid Composition Type-3A (PseKRAAC_T3A)
Pseudo K_tuple Reduced Amino Acid Composition Type_3B (PseKRAAC_T3B)
Pseudo K_tuple Reduced Amino Acid Composition Type-4 (PseKRAAC_T4)
Pseudo K_tuple Reduced Amino Acid Composition Type-5 (PseKRAAC_T5)
Pseudo K_tuple Reduced Amino Acid Composition Type-6A (PseKRAAC_T6A)
Pseudo K_tuple Reduced Amino Acid Composition Type-6B (PseKRAAC_T6B)
Pseudo K_tuple Reduced Amino Acid Composition Type-7 (PseKRAAC_T7)
Pseudo K_tuple Reduced Amino Acid Composition Type-8 (PseKRAAC_T8)
Pseudo K_tuple Reduced Amino Acid Composition Type-9 (PseKRAAC_T9)
Position-Specific Scoring Matrix (PSSM)
Position-Specific Trinucleotide Propensity based on double-strand (PST...
Position-Specific Trinucleotide Propensity based on single-strand DNA ...
Position-Specific Tri-ribonucleotide Propensity based on single-strand...
Quasi Sequence Order (QSOrder)
Read Directory of Accessible Solvent accessibility predicted files (re...
Read disorder predicted Directory (readDisDir)
Read PSSM Directory (readPSSMdir)
Read ss2 predicted Directory (readss2Dir)
Read Directory of Torsion predicted files (readTorsionDir)
reverseCompelement (revComp)
Splitted Amino Acid Composition (SAAC)
Splitted Group Amino Acid Composition (SGAAC)
Sequence Order Coupling Number (SOCNumber)
Secondary Structure Elements Binary (SSEB)
Secondary Structure Elements Composition (SSEC)
Secondary Structure Elements Simple (SSES)
Torsion Angle (TorsionAngle)
Trinucleotide physicochemical properties (TPCP_DNA)
Tri Nucleotide Index (TriNucIndex)
Z_curve_12bit_DNA (Zcurve12bit_DNA)
Z_curve_12bit_RNA (Zcurve12bit_RNA)
Z_curve_144bit_DNA (Zcurve144bit_DNA)
Z_curve_144bit_RNA (Zcurve144bit_RNA)
Z_curve_36bit_DNA (Zcurve36bit_DNA)
Z_curve_36bit_RNA (Zcurve36bit_RNA)
Z_curve_48bit_DNA (Zcurve48bit_DNA)
Z_curve_48bit_RNA (Zcurve48bit_RNA)
Z_curve_9bit_DNA (Zcurve9bit_DNA)
Z_curve_9bit_RNA (Zcurve9bit_RNA)
Z-SCALE (zSCALE)
Extracts features from biological sequences. It contains most features which are presented in related work and also includes features which have never been introduced before. It extracts numerous features from nucleotide and peptide sequences. Each feature converts the input sequences to discrete numbers in order to use them as predictors in machine learning models. There are many features and information which are hidden inside a sequence. Utilizing the package, users can convert biological sequences to discrete models based on chosen properties. References: 'iLearn' 'Z. Chen et al.' (2019) <DOI:10.1093/bib/bbz041>. 'iFeature' 'Z. Chen et al.' (2018) <DOI:10.1093/bioinformatics/bty140>. <https://CRAN.R-project.org/package=rDNAse>. 'PseKRAAC' 'Y. Zuo et al.' 'PseKRAAC: a flexible web server for generating pseudo K-tuple reduced amino acids composition' (2017) <DOI:10.1093/bioinformatics/btw564>. 'iDNA6mA-PseKNC' 'P. Feng et al.' 'iDNA6mA-PseKNC: Identifying DNA N6-methyladenosine sites by incorporating nucleotide physicochemical properties into PseKNC' (2019) <DOI:10.1016/j.ygeno.2018.01.005>. 'I. Dubchak et al.' 'Prediction of protein folding class using global description of amino acid sequence' (1995) <DOI:10.1073/pnas.92.19.8700>. 'W. Chen et al.' 'Identification and analysis of the N6-methyladenosine in the Saccharomyces cerevisiae transcriptome' (2015) <DOI:10.1038/srep13859>.