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QSLiMFinder specifications

Information


Unique identifier OMICS_07770
Name QSLiMFinder
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
License GNU General Public License version 2.0
Computer skills Advanced
Stability Stable
Maintained Yes

Subtool


  • SLiMSuite

Versioning


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Maintainer


  • person_outline Richard J. Edwards <>

Additional information


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Publication for QSLiMFinder

QSLiMFinder in publications

 (4)
PMCID: 5753338
PMID: 29136216
DOI: 10.1093/nar/gkx1077

[…] life science community. users are also encouraged to visit the ‘external links’ page (http://elm.eu.org/infos/links.html) which lists many other useful tools and databases for slim research such as qslimfinder (for motif discovery ()) and proviz (for motif exploration ()). we also welcome any feedback you can give us that can help us improve elm., we would like to thank all of the users of elm […]

PMCID: 5551000
PMID: 28793925
DOI: 10.1186/s40168-017-0307-1

[…] and virulence factors protein sequences to detect the presence of pfam domains [] (release 26). we kept only pfam-a matches with an e value <10−5., we used the slimsearch 2.0 tool from the slimsuite [] to identify occurrences of known short linear motifs from the elm database [] (downloaded in may 2013) in the f. nucleatum proteome. to select putative mimicry motifs, we applied two […]

PMCID: 4878775
PMID: 27218803
DOI: 10.1371/journal.pone.0155911

[…] further experimental studies on them. meme was chosen for the motif identification step because it does not adjust for evolutionary relationships, (unlike dilimot[], slimdisc[], slimfinder[] and qslimfinder[]) therefore accounting for sequence patterns responsible for ppis in evolutionarily related proteins []. a scoring system was also formulated to rank the predicted olps according […]

PMCID: 2819990
PMID: 20055997
DOI: 10.1186/1471-2105-11-14

[…] command line switches introduced for the two calculations (sigprime = t/f and sigv = t/f)., the programme is available at http://bioinformatics.ucd.ie/shields/software/slimfinder. the version of the slimsuite software package available at time of submission is also included as supplemental information with this paper (additional file )., when tested on randomly created datasets, significance […]


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QSLiMFinder institution(s)
Centre for Biological Sciences, University of Southampton, Southampton, UK

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