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About

SLiMSearch is a short, linear motif (SLiM) discovery tool. The tool searches a proteome using a motif consensus to discover putative novel motif instances. Motif attributes known to be strong discriminators of motif functionality, such as accessibility and conservation, are calculated for each instance. Instances are also annotated with experimental, proteomic and genomic data. The tool also allows instance filtering based on keyword, interaction, localisation information. In depth ontology enrichment and conservation analysis tools are also available. Find a tutorial to understand the SLiMSearch output here.

Reference:
"SLiMSearch - a framework for proteome-wide discovery and annotation of functional modules in intrinsically disordered regions"
Izabella Krystkowiak and Norman E. Davey
Nucleic Acids Res. 2017 Apr 6. (Epub ahead of print).


Jobs are stored for two weeks.

Search details


Format: WRPW motif example
Format
The motif consensus search uses a regular expressions to scan proteomes. The motif regular expressions are defined with single-letter amino acid codes following the ELM resource motif definitions. Examples and guidelines are below.

Examples
Motif Consensus
KEN box motif KEN
Cyclin-binding RxL motif [KR].L.{0,1}[LF]
C-terminal KDEL Golgi-to-ER retrieving signal [KRHQSAP][DENQT]EL$
N-terminal myristoylation site ^M{0,1}G[^EDRKHPFYW]..[STAGCN][^P]

Special characters
Character Name Meaning
. dot Any amino acid allowed
[...] character class Amino acids listed are allowed
[^...] negated character class Amino acids listed are not allowed
{ min, max } specified range Min required, max allowed
^ caret Matches the amino terminal
$ dollar Matches the carboxy terminal
 

Choose species: Homo sapiens
Homo sapiens Xenopus tropicalis Drosophila melanogaster Caenorhabditis elegans
Saccharomyces cerevisiae Schizosaccharomyces pombe Arabidopsis thaliana + more
 

Choose options
Disorder score cut-off : 0.40
Flank length : 5
 

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