protr
Comprehensive toolkit for generating various numerical representation schemes of protein sequence. The descriptors included in the protr package are extensively utilized in bioinformatics and chemogenomics.
Descriptors List
Commonly used descriptors
Amino acid composition
- Amino acid composition
- Dipeptide composition
- Tripeptide composition
Autocorrelation
- Normalized Moreau-Broto autocorrelation
- Moran autocorrelation
- Geary autocorrelation
CTD
- Composition
- Transition
- Distribution
Conjoint Triad
Quasi-sequence-order descriptors
- Sequence-order-coupling number
- Quasi-sequence-order descriptors
Pseudo amino acid composition
- Pseudo amino acid composition
- Amphiphilic pseudo amino acid composition
Profile-based descriptors
- Profile-based descriptors derived by PSSM (Position-Specific Scoring Matrix)
Proteochemometric (PCM) modeling descriptors
- Scales-based descriptors derived by principal components analysis
- Scales-based descriptors derived by amino acid properties (AAindex)
- Scales-based descriptors derived by 20+ classes of 2D and 3D molecular descriptors (Topological, WHIM, VHSE, etc.)
- Scales-based descriptors derived by factor analysis
- Scales-based descriptors derived by multidimensional scaling
- BLOSUM and PAM matrix-derived descriptors
Similarity Computation
Local and global pairwise sequence alignment for protein sequences:
- Between two protein sequences
- Parallelized pairwise similarity calculation with a list of protein sequences
GO semantic similarity measures:
- Between two groups of GO terms / two Entrez Gene IDs
- Parallelized pairwise similarity calculation with a list of GO terms / Entrez Gene IDs
Miscellaneous tools and datasets
- Retrieve protein sequences from UniProt
- Read protein sequences in FASTA format
- Read protein sequences in PDB format
- Sanity check of the amino acid types appeared in the protein sequences
- Protein sequence segmentation
- Auto cross covariance (ACC) for generating scales-based descriptors of the same length
- 20+ pre-computed 2D and 3D descriptor sets for the 20 amino acids to use with the scales-based descriptors
- BLOSUM and PAM matrices for the 20 amino acids
- Meta information of the 20 amino acids
Web Server
ProtrWeb, the web server built on protr, is located at:
ProtrWeb does not require any knowledge of R programming for the users, it is a user-friendly and one-click-to-go online platform for computing the descriptors presented in the protr package.
Paper Citation
Formatted citation:
Nan Xiao, Dong-Sheng Cao, Min-Feng Zhu, and Qing-Song Xu. (2015). protr/ProtrWeb: R package and web server for generating various numerical representation schemes of protein sequences. Bioinformatics 31 (11), 1857-1859.
BibTeX entry:
@article{Xiao2015,
author = {Xiao, Nan and Cao, Dong-Sheng and Zhu, Min-Feng and Xu, Qing-Song.},
title = {{protr/ProtrWeb: R package and web server for generating various numerical representation schemes of protein sequences}},
journal = {Bioinformatics},
year = {2015},
volume = {31},
number = {11},
pages = {1857--1859},
doi = {10.1093/bioinformatics/btv042},
issn = {1367-4803},
url = {http://bioinformatics.oxfordjournals.org/content/31/11/1857}
}