PROMPT-Protein Mapping and Comparison Tool

PROMPT: Protein Mapping and Comparison Tool

PROMPT is a platform independent system for retrieval, analysis, mapping and comparison of protein sets. It allows easy mapping of different types of sequence identifiers, automatical data retrieval and integration, a multitude of analysis and comparison algorithms and a full-featured easy to use graphical user interface (GUI) application with an integrated help-system. Moreover exhaustive statistical tests are conducted in appropriate cases automatically or could be performed manually. Furthermore all analysis results can be viewed or visualized with one mouse-click and exported in various formats e.g. to Microsoft Excel. Additionally all methods can be used easily in your own Java code or with powerful beanshell scripting in own scripts, a pipeline or grid systems.

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Screenshots

Case Studies

PROMPT reference

Schmidt, T., Frishman, D. (2006), PROMPT: a protein mapping and comparison tool,
BMC Bioinformatics 2006, 7:331; Link

Publications that cite PROMPT

Coupling a Detergent Lysis/Cleanup Methodology with Intact Protein Fractionation for Enhanced Proteome Characterization
Sharma, R et al.
J. PROTEOME RES. 2012, 11 (12), pp 6008 - 6018
DOI: 10.1021/pr300709k

Bacterial protein structures reveal phylum dependent divergence.
Shortridge, MD et al.
COMPUT. BIOL. CHEM.2011 Feb;35(1):24-33.
DOI: 10.1016/j.compbiolchem.2010.12.004

Probing the Phosphoproteome of HeLa Cells Using Nanocast Metal Oxide Microspheres for Phosphopeptide Enrichment
Leitner, A et al.
ANALYTICAL CHEMISTRY, 82 (7): 2726-2733 APR 1 2010
DOI: 10.1021/ac902560z

Helicobacter pylori proteomics by 2-DE/MS, 1-DE-LC/MS and functional data mining
Jungblut, PR et al.
PROTEOMICS, 10 (2): 182-193 JAN 2010
DOI: 10.1002/pmic.200900361

Urinary Proteomics Evaluation in Interstitial Cystitis/Painful Bladder Syndrome: A Pilot Study
Tseng, LH (Tseng, Ling-Hong)
INTERNATIONAL BRAZ J UROL, 36 (4): 478-479 JUL-AUG 2010, EDITORIAL COMMENT

Differential substrate specificity of group I and group II chaperonins in the archaeon Methanosarcina mazei
Hirtreiter, AM et al.
MOLECULAR MICROBIOLOGY, 74 (5): 1152-1168 DEC 2009
DOI: 10.1111/j.1365-2958.2009.06924.x

Sequence-Based Prediction of Type III Secreted Proteins
Arnold, R et al.
PLOS PATHOGENS, 5 (4): Art. No. e1000376 APR 2009
DOI: 10.1371/journal.ppat.1000376

Protein abundance profiling of the Escherichia coli cytosol
Ishihama Y, Schmidt T, Rappsilber J, et al.
BMC GENOMICS Volume: 9 Article Number: 102 Published: FEB 27 2008
DOI: 10.1186/gb-2008-9-6-r104

An evolutionary and structural characterization of mammalian protein complex organization
Wong, P et al.
BMC GENOMICS, 9: Art. No. 629 DEC 23 2008
DOI: 10.1186/1471-2164-9-629

OREST - Online resource for EST analysis
Wägele B, Schmidt T, Ruepp A, Mewes HW
NUCLEIC ACIDS RESEARCH, 36: W140-W144 Suppl. S JUL 2008
DOI: 10.1093/nar/gkn253

An approach to handling and interpretation of ambiguous data in transcriptome and proteome comparisons
Irmler M, Hartl D, Schmidt T, et al.
PROTEOMICS, 8 (6): 1165-1169 MAR 2008
DOI: 10.1002/pmic.200700741

The fungus Ustilago maydis and humans share disease-related proteins that are not found in Saccharomyces cerevisiae
Munsterkotter M, Steinberg G
BMC GENOMICS, 8: Art. No. 473 DEC 20 2007
DOI: 10.1186/1471-2164-8-473

Assignment of isochores for all completely sequenced vertebrate genomes using a consensus
Schmidt, T; Frishman, D
GENOME BIOLOGY, 9 (6): Art. No. R104 2008
DOI: 10.1186/gb-2008-9-6-r104

SIMAPstructuring the network of protein similarities
Rattei T, Tischler P, Arnold R, et al.
NUCLEIC ACIDS RESEARCH Volume: 36 Special Issue: Sp. Iss. SI Pages: D289-D292 Published: JAN 2008
DOI: 10.1093/nar/gkm963

The Protein Identifier Cross-Referencing (PICR) service: reconciling protein identifiers across multiple source databases
Cote RG, Jones P, Martens L, et al.
BMC BIOINFORMATICS Volume: 8 Article Number: 401 Published: OCT 18 2007
DOI: 10.1186/1471-2105-8-401

Bioinformatics for study of autoimmunity.
Petrovsky N, Brusic V.
AUTOIMMUNITY. 2006 Dec;39(8):635-43.

PEDANT genome database: 10 years online.
Riley ML, Schmidt T, Artamonova II, Wagner C, Volz A, Heumann K, Mewes HW, Frishman D.
NUCLEIC ACIDS RESEARCH 2006 Dec 5
DOI: 10.1093/nar/gkl1005

DnaK Functions as a Central Hub in the E. coli Chaperone Network.
Chen Taotao
Dissertation, LMU Muenchen: Faculty of Chemistry and Pharmacy 12. December 2011
http://nbn-resolving.de/urn:nbn:de:bvb:19-137848

Development and application of computational methdologies for Integrated Molecular Systems Biology
Karathia, Hiren Mahendrabhai
PhD thesis, Universitat de Lleida. Departament de Ciencies Mediques Basiques 2012-11-30
http://hdl.handle.net/10803/110518

TOOLbox - PROMPT for comparisons,
Vol. 5, No. 9: September 2006; pp 2072–2073;
JOURNAL OF PROTEOME RESEARCH (2006)
Web-version, PDF-screen, PDF-print, About the journal