Pages: |
Help:Help OverviewMain Help
Walkthrough of example SLiMSearch analysis with screenshots. Manual - (PDF) Manual for the standalone version of SLiMSearch in pdf format. May contain details which may not be obvious from the server implentation of the program. User-group SLiMFinder user-group for additional community support. Example Input Example UniProt input file for proteins containing the Dynein light chain interaction motif. Example Output Fully functional results page corresponding to example input run with default options References and Citations Papers to cite when using results in publications. Standard analysis
Sequence information input filesNB. For custom (UniProt) datasets, the SLiMSearch server is limited to 100 sequences. Evolutionary filtering is not available for genomic datasets.Examples of acceptable input formats are available here: UniProt format FASTA format Two methods of sequence selection entry are possible: UniProt Ids The right hand panel of the inputs section allows a list of UniProt Ids to be entered. These Ids will be fetched and used as the input data for SLiMSearch. For full functionality (including RLC masking) it is advised that user enter proteins data in this way. or Human proteome datasets The SLiMSearch server also permits searching of the UniProt Human proteome. This can also be limited to specific subsets (nuclear, cytoplasmic, transmembrane) based on keywords in UniProt. Motif inputOnce a dataset has been selected, the user must input a set of motifs to search. The SLiMSearch server takes a list of motifs, typed or pasted directly into the text box. Motifs themselves are constructed from a number of regular expression elements, which are mostly standard but with a couple of additional elements to represent "3of5" motifs:
SLiMSearch accepts the same input formats as CompariMotif, including a plain list of regular expressions and output from SLiMDisc or SLiMFinder. Because the focus of SLiMSearch is short linear motifs, the maximum number of consecutive wildcards allowed by the server is nine. Motifs must have at least two defined (i.e. non-wildcard) positions. Masking OptionsDisorder maskingSLiMs tend to occur in disordered regions of proteins. The SLiMSearch server uses IUPRED (Dosztanyi et al. 2005) to predict regions of disorder with a relaxed score cut-off of 0.2. Residues predicted to be "intrinsically ordered" are masked out. This can be toggled on/off.Conservation maskingBy default conservation masking is used, metazoan orthologues are retrieved and masking of underconserved residues is carried out. For more details see:
Davey NE, Shields DC & Edwards RJ (2009): Feature maskingDefined UniProt features can be maskeds, areas such as transmembrane regions, protein domains and inaccessible residues can be masked as they are areas which have a low likelihood of containing motifs.The same mechanism used for masking these region also allow the user identify specific regions of the proteins in which to confine the search , for example the user may wish to look at motifs which are occurring in the cytoplasmic regions of a set of proteins or may have prior knowledge of a region possibly containing a functional motif. There are two types of feature masking in SLiMSearch: Inclusive masking and Exclusive masking:
Inclusive masking is preformed first. This means that exclusively masked regions appearing inside an inclusively masked region will be removed. Masking is based on UniProt features:
Output DescriptionAn example results output for a Dynein Light Chain binding protein dataset is available here and in the screenshot walkthrough.References and CitationsWhen using SLiMSearch results in a publication, please cite this webserver. (The publication is currently under review.) In addition, SLiMSearch uses the following underlying software:
If using IUPRED disorder prediction to mask input sequences and/or filter results, please cite:
If using Relative Local Conservation masking, in addition to the GOPHER citations (below) please cite:
If using alignments of homologous proteins, generated by GOPHER, please cite:
If using the SLiMChance evolutionary filtering, please cite:
Contributing LabsThis server is hosted by the Clinical Bioinformatics group led by Prof. Denis Shields in the Conway Institute of Biomolecular and Biomedical Research. The tools have been developed by Rich Edwards (currently at The University of Southampton) and Norman Davey (currently at EMBL Heidelberg). This project is a collaboration between 3 institutions, Conway Institute of Biomolecular and Biomedical Research at University College Dublin (Dublin, Ireland), School of Biological Science at University of Southampton (Southampton, England) and European Molecular Biology Laboratories (Heidelberg, Germany). Q.
Why can I only use conservation masking for UniProt entries downloaded through your site?
|