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SearchGUI specifications
Information
| Unique identifier | OMICS_03352 |
|---|---|
| Name | SearchGUI |
| Software type | Package/Module |
| Interface | Command line interface, Graphical user interface |
| Restrictions to use | None |
| Operating system | Unix/Linux, Mac OS, Windows |
| Programming languages | Java, Perl |
| License | Apache License version 2.0 |
| Computer skills | Advanced |
| Version | 3.3.3 |
| Stability | Stable |
| Maintained | Yes |
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Versioning
No version available
Documentation
Maintainer
- person_outline Marc Vaudel <>
Additional information
Publications for SearchGUI
SearchGUI: A Highly Adaptable Common Interface for Proteomics Search and de Novo Engines.
SearchGUI: An open-source graphical user interface for simultaneous OMSSA and X!Tandem searches.
SearchGUI citations
(38)Identification of a unique Radical SAM methyltransferase required for the sp3 C methylation of an arginine residue of methyl coenzyme M reductase
[…] acquired in the orbitrap at a resolution of 60,000 and a maximum injection time of 120 ms for orbitrap ms2 detection., the raw mass spectrometric data were converted to mgf-files using msconvert. searchgui software (v3.2.17) and the omssa search engine were used for peptide identification. the data were searched against the m. acetivorans proteome database obtained from uniprot (taxon […]
Hookworm Secreted Extracellular Vesicles Interact With Host Cells and Prevent Inducible Colitis in Mice
[…] of adventitious proteins (crap) appended to it. database search was performed using mascot versions 2.4 (matrix science ltd., london, uk) and x!tandem, ms-gf+, omssa, and tide search engines using searchgui (). the same parameters were used as described in ref. ()., the mass spectrometry proteomics data have been deposited in the proteomexchange consortium via the pride partner repository […]
Intrinsically disordered N termini in human parechovirus 1 capsid proteins bind encapsidated RNA
[…] accela hplc. peptide rcap data was generated on a bruker autoflex iii maldi-tof and analyzed using gpmaw (general protein/mass analysis for windows, supplementary figure )., database searches used searchgui and the peptide sequences were compiled with peptideshaker,. databases were created using hpev1 protein sequences appended to a fasta file containing the uniprot human proteome […]
A graphical user interface for RAId, a knowledge integrated proteomics analysis suite with accurate statistics
[…] to integrate with raid useful visualization and graphic tools, we have developed the first gui for raid. although there exist other freely available proteomics analysis gui such as omssagui [] and searchgui [], raid_gui is the only one that provides not only peptide/protein identifications with accurate statistics but also a large collection of additional functionalities., to run raid_gui […]
Disseminating Metaproteomic Informatics Capabilities and Knowledge Using the Galaxy P Framework
[…] the use of de novo spectral matching in tandem with traditional sequence database-dependent methods [], as well as the use of multiple database search algorithms, such as those offered by the searchgui tool [], to increase the numbers of confident metapeptide identifications. , for the workflow deployed in our informatics resource, we chose a relatively straightforward approach […]
Homeolog expression analysis in an allotriploid non model crop via integration of transcriptomics and proteomics
[…] (crap, http://www.thegpm.org/crap/) and combined into a target/decoy database enabling false discovery rate (fdr) estimation. the decoy sequences were created by reversing the target sequences in searchgui v 3.1.4,., for every sample, peak lists (.mgf format) containing all msms spectra were extracted from progenesis and were identified against its proper database integrating 3 database […]
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