Short, linear motif prediction software tools | Protein sequence data analysis
Short, linear motifs (SLiMs) are short stretches of protein sequences generally located in intrinsically disordered regions (IDRs); these sites are targets for cleavage, posttranslational modifications and ligand-binding modules in protein-protein interactions.
Gives access to many free software tools for sequence analysis. EMBOSS aims to serve the molecular biology community. It permits the creation and the release of software in an open source spirit. This tool is useful for sequence analysis into a seamless whole. It is free of charge and is available in open source.
An integrated service dedicated to the analysis of protein sequences. Since its first description in 2004, both the user interface and the back end of the server were improved. A number of tools (e.g. MAFFT, Jacop, Dotlet, Jalview, ESTScan) were added or updated to improve the usability of the service.
A server for the prediction of these short linear motifs within a set of proteins. Given a set of sequences sharing a common functional feature (e.g. interaction partner or localization) the method finds statistically over-represented motifs likely to be responsible for it. The input sequences are first passed through a set of filters to remove regions unlikely to contain instances of linear motifs. Motifs are then found in the remaining sequence and ranked according to a statistic that measure over-representation and conservation across homologues in related species. The results are displayed via a visual interface for easy perusal.
Allows motif consensus search, annotation and filtering. SLiMSearch is a web-based tool for the discovery of novel short linear motifs (SLiM) instances in a proteome. The framework searches characterized motif specificity determinants to identify putative novel motif instances which are annotated with accessibility information, evolutionary attributes and experimental information. The software can aid biologists in building hypotheses and designing experiments by simplifying the analysis of the functional and evolutionary features of motifs.
Combines hidden Markov model (HHM) comparisons with a hierarchical representation of identified SLiMs in motif trees. HH-MOTiF is a web-server that can find remotely conserved motifs in data sets with low-complexity regions or high redundancy. It makes use of evolutionary information by creating HMMs for each input sequence and its orthologs. Finally, this method can detect several independent motif trees that occur in independent, possibly overlapping subsets of the provided input sequences.
Takes two lists of regular expression protein (or DNA) motifs and compares them to each other, identifying which motifs have some degree of overlap. CompariMotif outputs a table of all pairs of matching motifs, along with their degree of similarity (information content) and their relationship to each other.
A manually curated database of short linear motifs (SLiMs). ELM 2016 contains more than 240 different motif classes with over 2700 experimentally validated instances, manually curated from more than 2400 scientific publications. In addition, more data have been made available as individually searchable pages and are downloadable in various formats.