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Protocols

CRASP specifications

Information


Unique identifier OMICS_25741
Name CRASP
Alternative name correlation analysis of protein sequences
Interface Web user interface
Restrictions to use None
Input format FASTA
Computer skills Basic
Version 1.1.0
Stability Stable
Maintained Yes

Maintainers


  • person_outline Dmitry Afonnikov
  • person_outline Nikolay Kolchanov

Publication for correlation analysis of protein sequences

CRASP citations

 (6)
library_books

SubVis: an interactive R package for exploring the effects of multiple substitution matrices on pairwise sequence alignment

2017
PeerJ
PMCID: 5490468
PMID: 28674656
DOI: 10.7717/peerj.3492

[…] r-to-pair substitution matrices. However, it is designed for a specific custom matrix type, does not provide standard matrices, and lacks features that facilitate comparison among different matrices. CRASP () is a web-accessible tool that takes protein family sequence alignments, a phylogenetic tree or other weights, physicochemical characteristics, and conservation filters as input. The output co […]

call_split

Origins and Evolution of WUSCHEL Related Homeobox Protein Family in Plant Kingdom

2014
Sci World J
PMCID: 3913392
PMID: 24511289
DOI: 10.1155/2014/534140
call_split See protocol

[…] Analysis of pairwise positional correlations was obtained from the Correlation Analysis of Protein Sequences (CRASP) database with the default parameter setting. […]

library_books

The Role of Insulin C Peptide in the Coevolution Analyses of the Insulin Signaling Pathway: A Hint for Its Functions

2012
PLoS One
PMCID: 3531361
PMID: 23300796
DOI: 10.1371/journal.pone.0052847

[…] (e.g., charge, volume, polarity, and hydrophobicity) , allows inferences to be made about the structural–functional role of residues at these positions and to predict protein structure , . The CRASP (Correlation analysis of protein sequences) program is based on estimation of the correlation coefficient between the values of a physicochemical parameter at a pair of positions of sequence alignment. […]

library_books

Sequence Complexity of Chromosome 3 in Caenorhabditis elegans

2012
Adv Bioinformatics
PMCID: 3418640
PMID: 22919380
DOI: 10.1155/2012/287486

[…] been observed and measured in pathology and cancer models [, ], the study of branching blood vessels, or the irregularity of the contours of tumor cells [, ], the analysis of complete genomes [], the correlation analysis of protein sequences [] tissue pathology [], in exons, introns [], and nuclei [], and it is involved in blood cancer [, ]. […]

library_books

Hyperdimensional Analysis of Amino Acid Pair Distributions in Proteins

2011
PLoS One
PMCID: 3235099
PMID: 22174733
DOI: 10.1371/journal.pone.0025638

[…] open source tools or through user friendly interfaces. Only a few programs have been implemented to date on the web –. Some programs can be downloaded for local usage, such as PlotCor , CorrMut and CRASP . CysView is a web-based application tool that displays cysteine connectivity patterns in proteins . ESBRI is a web tool which analyses the salt bridges in a protein structure . However, the gen […]

call_split

Positive and Negative Design in Stability and Thermal Adaptation of Natural Proteins

2007
PLoS Comput Biol
PMCID: 1829478
PMID: 17381236
DOI: 10.1371/journal.pcbi.0030052
call_split See protocol

[…] n a) by using Kalign Web-server for multiple alignment of protein sequences (http://msa.cgb.ki.se/cgi-bin/msa.cgi, []).Correlated substitutions in the multiple alignments were determined by using the CRASP program (http://wwwmgs.bionet.nsc.ru/mgs/programs/crasp, []). The CRASP program gives the correlation coefficient between the values of physicochemical parameters at a pair of positions of seque […]

Citations

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CRASP institution(s)
Institute of Cytology and Genetics, SB RAS, Novosibirsk, Russia; The Novosibirsk State University, Novosibirsk, Russia
CRASP funding source(s)
Supported by grants from the Russian Foundation for Basic Research (03-07-96833-p2003, 03-07-96833) and the Siberian Branch of the Russian Academy of Sciences (project No. 148, 119), the Russian Ministry of Industry, Sciences and Technologies (No. 43.073.1.1.1501, subcontract 28/2003), MCB RAS (No. 10.4), the CRDF and the Ministry of Education of the Russian Federation within the Basic Research and Higher Education Program (Y1-B-08-20, NO-008-X1).

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