Composition Profiler statistics

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Composition Profiler specifications

Information


Unique identifier OMICS_25832
Name Composition Profiler
Interface Web user interface
Restrictions to use None
Input data Some protein sequences.
Input format FASTA
Programming languages C, C++, Ruby
License MIT License
Computer skills Basic
Stability Stable
Maintained Yes

Maintainers


  • person_outline Stefano Lordi
  • person_outline Vladimir Vacic
  • person_outline Vladimir Uversky
  • person_outline Keith Dunker

Additional information


http://www.cprofiler.org/cgi-bin/profiler.cgi http://www.cprofiler.org/help.html

Information


Unique identifier OMICS_25832
Name Composition Profiler
Software type Application/Script
Interface Command line interface
Restrictions to use None
Input data Some protein sequences.
Input format FASTA
Operating system Unix/Linux, Mac OS
Programming languages C, C++, Ruby
License MIT License
Computer skills Advanced
Version 1.1
Stability Stable
Requirements
GhostScript, ImageMagick, gnuplot
Maintained Yes

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Versioning


No version available

Maintainers


  • person_outline Stefano Lordi
  • person_outline Vladimir Vacic
  • person_outline Vladimir Uversky
  • person_outline Keith Dunker

Additional information


http://www.cprofiler.org/cgi-bin/profiler.cgi http://www.cprofiler.org/help.html

Publication for Composition Profiler

Composition Profiler citations

 (28)
call_split

Bioinformatic Analysis Reveals Conservation of Intrinsic Disorder in the Linker Sequences of Prokaryotic Dual family Immunophilin Chaperones

2017
Comput Struct Biotechnol J
PMCID: 5852385
PMID: 29552333
DOI: 10.1016/j.csbj.2017.12.002
call_split See protocol

[…] Amino acid composition of the linkers was determined by the use of Composition Profiler (www.cprofiler.org), a web-based tool that automates detection of enrichment or depletion patterns of amino acids classified by user-chosen properties []. For the linker analysis, […]

library_books

Prediction of endoplasmic reticulum resident proteins using fragmented amino acid composition and support vector machine

2017
PeerJ
PMCID: 5588793
PMID: 28890846
DOI: 10.7717/peerj.3561

[…] ar location is specifically adopted to suit its surrounding environment (). In order to understand this pattern in case of ERRPs, we analysed the enrichment and depletion pattern of amino acids using Composition Profiler (). Composition Profiler detects the enrichment and depletion patterns of individual amino acid as well as group of amino acids classified on the basis of different physico-chemic […]

call_split

Intrinsic Disorder of the C Terminal Domain of Drosophila Methoprene Tolerant Protein

2016
PLoS One
PMCID: 5033490
PMID: 27657508
DOI: 10.1371/journal.pone.0162950
call_split See protocol

[…] Disorder predictions were made using the IUPred server [,] available at http://iupred.enzim.hu. Amino acid composition analyses were performed using the Composition Profiler available at http://www.cprofiler.org [,]. The Uversky plot [], VSL2 [,], PONDR-FIT [], DISOPRED2 [] and FoldIndex [] calculations were made using PONDR at http://www.pondr.com. G […]

library_books

Is unphosphorylated Rex, as multifunctional protein of HTLV 1, a fully intrinsically disordered protein? An in silico study

2016
PMCID: 5613702
PMID: 28955936
DOI: 10.1016/j.bbrep.2016.07.018

[…] evels allow to specifically low affinity interactions , , . Rex Protein flexibility analysis was performed by Expasy server using an average flexibility scale, DynaMine server (data not be shown) and Composition Profiler server was performed. They showed high flexibility areas that interrupted by short regions with less flexibility levels (). Based on Rex flexibility results, Rex is a protein with […]

library_books

A widely employed germ cell marker is an ancient disordered protein with reproductive functions in diverse eukaryotes

2016
eLife
PMCID: 5098910
PMID: 27718356
DOI: 10.7554/eLife.19993.029

[…] Amino acid compositional analysis was carried out using Composition Profiler ()(RRID:SCR_014630, http://www.cprofiler.org) using the PDB Select 25 and the DisProt datasets as reference for ordered and disordered proteins, respectively. Enrichment or deplet […]

library_books

The alveolate translation initiation factor 4E family reveals a custom toolkit for translational control in core dinoflagellates

2015
BMC Evol Biol
PMCID: 4330643
PMID: 25886308
DOI: 10.1186/s12862-015-0301-9

[…] est to compare the amino acid composition of each alignment row with the empirical frequencies calculated from the alignment []. The amino acid bias for specific clades was further explored using the composition profiler tool [].Sequence logos were created using WebLogo [] for each core dinoflagellate clade by trimming outgroup taxa and creating clade specific alignments. The amino acid sequences […]

Citations

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Composition Profiler institution(s)
Department of Computer Science and Engineering, University of California, Riverside, CA, USA; Center for Computational Biology and Bioinformatics, Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN, USA; Institute for Biological Instrumentation, Russian Academy of Sciences, Pushchino, Russia
Composition Profiler funding source(s)
Supported in part by NSF CAREER IIS-0447773, and NSF DBI-0321756.

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