Generating Various Numerical Representation Schemes for Protein Sequences
Auto Cross Covariance (ACC) for Generating Scales-Based Descriptors of...
Parallel Protein Sequence Similarity Calculation Between Two Sets Base...
Parallel Protein Sequence Similarity Calculation Between Two Sets Base...
Amino Acid Composition Descriptor
Amphiphilic Pseudo Amino Acid Composition (APseAAC) Descriptor
BLOSUM and PAM Matrix-Derived Descriptors
CTD Descriptors - Composition
CTD Descriptors - Composition (with customized amino acid classificati...
CTD Descriptors - Distribution
CTD Descriptors - Distribution (with customized amino acid classificat...
CTD Descriptors - Transition
CTD Descriptors - Transition (with customized amino acid classificatio...
Conjoint Triad Descriptor
Conjoint Triad Descriptor (with customized amino acid classification s...
Dipeptide Composition Descriptor
Scales-Based Descriptors with 20+ classes of Molecular Descriptors
Scales-Based Descriptors derived by Factor Analysis
Geary Autocorrelation Descriptor
Scales-Based Descriptors derived by Multidimensional Scaling
Moran Autocorrelation Descriptor
Normalized Moreau-Broto Autocorrelation Descriptor
Pseudo Amino Acid Composition (PseAAC) Descriptor
Amino Acid Properties Based Scales Descriptors (Protein Fingerprint)
Amino Acid Properties Based Scales Descriptors (Protein Fingerprint) w...
Compute PSSM (Position-Specific Scoring Matrix) for given protein sequ...
Profile-based protein representation derived by PSSM (Position-Specifi...
Profile-based protein representation derived by PSSM (Position-Specifi...
Quasi-Sequence-Order (QSO) Descriptor
Scales-Based Descriptors derived by Principal Components Analysis
Scales-Based Descriptors derived by Principal Components Analysis (wit...
Sequence-Order-Coupling Numbers
Tripeptide Composition Descriptor
Retrieve Protein Sequences from UniProt by Protein ID
OptAA3d.sdf - 20 Amino Acids Optimized with MOE 2011.10 (Semiempirical...
Protein Similarity Calculation based on Gene Ontology (GO) Similarity
Parallel Protein Sequence Similarity Calculation Based on Sequence Ali...
Parallel Protein Sequence Similarity Calculation Based on Sequence Ali...
Protein sequence amino acid type sanity check
protr: Generating Various Numerical Representation Schemes for Protein...
Protein Sequence Segmentation/Partition
Read Protein Sequences in FASTA Format
Read Protein Sequences in PDB Format
Remove or replace gaps from protein sequences.
Protein Similarity Calculation based on Gene Ontology (GO) Similarity
Protein Sequence Alignment for Two Protein Sequences
Comprehensive toolkit for generating various numerical features of protein sequences described in Xiao et al. (2015) <DOI:10.1093/bioinformatics/btv042>. For full functionality, the software 'ncbi-blast+' is needed, see <https://blast.ncbi.nlm.nih.gov/doc/blast-help/downloadblastdata.html> for more information.