tutorial arrow
×
Submit new tools
Share tools covering the current topic. Provide easy-to-follow guidelines to improve their usability.

Short, linear motif prediction software tools | Protein sequence 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…
DALEL
Web

DALEL

Searches the linear information in proteins. DALEL utilizes a novel parallel…

Searches the linear information in proteins. DALEL utilizes a novel parallel and recursive algorithm that allows divide the exploding space of enumeration and degeneration into much smaller spaces…

ELM
Web

ELM Eukaryotic Linear Motif resource

A manually curated database of short linear motifs (SLiMs). ELM 2016 contains…

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…

FIRE-pro
Desktop

FIRE-pro

Discovers protein motifs from large-scale proteomics datasets. FIRE-pro is a…

Discovers protein motifs from large-scale proteomics datasets. FIRE-pro is a methodology has a simple goal: to discover protein motifs whose presence or absence in protein sequences correlates with…

MyHits
Web

MyHits

An integrated service dedicated to the analysis of protein sequences. Since its…

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…

SLiMSearch
Web

SLiMSearch Short, Linear Motif Search

Allows motif consensus search, annotation and filtering. SLiMSearch is a…

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…

HH-MOTiF
Web

HH-MOTiF HH-MOtif-TreeFinder

Combines hidden Markov model (HHM) comparisons with a hierarchical…

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…

QSLiMFinder
Desktop

QSLiMFinder

A modification of the basic SLiMFinder tool to specifically look for SLiMs…

A modification of the basic SLiMFinder tool to specifically look for SLiMs shared by a query sequence and one or more additional sequences. To do this, SLiMBuild first identifies all motifs that are…

iELM
Web

iELM interactions of Eukaryotic Linear Motif

Provides a resource for predicting the function and positional interface for a…

Provides a resource for predicting the function and positional interface for a subset of interactions mediated by short linear motifs (SLiMs). The iELM prediction algorithm is based on the annotated…

DILIMOT
Web

DILIMOT DIscovery of LInear MOTifs

A server for the prediction of these short linear motifs within a set of…

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…

MAGIIC-PRO
Web

MAGIIC-PRO

Aims to discover functional signatures of a query protein by sequential pattern…

Aims to discover functional signatures of a query protein by sequential pattern mining. Automatic discovery of patterns from unaligned biological sequences is an important problem in molecular…

seeMotif
Web

seeMotif

Aims to visualize sequence motifs on 3D structures related to a given reference…

Aims to visualize sequence motifs on 3D structures related to a given reference protein. seeMotif provides an easy-to-use interface for submitting motifs in different formats. Visualizing the spatial…

SLiMPrints
Web

SLiMPrints Short Linear Motif fingerPrints

A de novo motif discovery tool. SLiMPrints identifies relatively…

A de novo motif discovery tool. SLiMPrints identifies relatively overconstrained proximal groupings of residues within intrinsically disordered regions, indicative of putatively functional motifs.

QuasiMotiFinder
Web

QuasiMotiFinder

A server for the identification of signatures and signature-like patterns in…

A server for the identification of signatures and signature-like patterns in protein sequences. QuasiMotiFinder is based on a search with an MSA of homologous query proteins against the original…

switches.ELM
Dataset

switches.ELM

Consists of a database that curates experimentally validated motif-based…

Consists of a database that curates experimentally validated motif-based molecular switches and a prediction tool to identify possible switching mechanisms that might regulate a user-submitted motif…

EPSLiM
Web

EPSLiM Ensemble Predictor for Short Linear Motifs

A strategy to prioritize the residues that are most likely to be short linear…

A strategy to prioritize the residues that are most likely to be short linear motifs (SLiMs) in intrinsically disordered regions (IDRs). EPSLiM applies a generalized linear model to integrate…

MotifHound
Desktop

MotifHound

An algorithm particularly suited for the discovery of small and degenerate…

An algorithm particularly suited for the discovery of small and degenerate linear motifs. MotifHound performs an exact and exhaustive enumeration of all motifs present in proteins of interest,…

CompariMotif
Desktop
Web

CompariMotif

Takes two lists of regular expression protein (or DNA) motifs and compares them…

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…

PMS
Web

PMS Panoptic Motif Search Tool

This tool will help you detect new unknown DNA motifs that may be present in…

This tool will help you detect new unknown DNA motifs that may be present in your input sequences. PMS has been helping scientists identify many unknown motifs.

SLiMScape
Desktop

SLiMScape

Provides a platform for performing short linear motif analyses of protein…

Provides a platform for performing short linear motif analyses of protein interaction networks by integrating motif discovery and search tools in a network visualization environment. SLiMScape aids…

fuzztran
Desktop

fuzztran

Searches for patterns in nucleic acid sequences that are first translated to…

Searches for patterns in nucleic acid sequences that are first translated to protein in the specified frame with a specified genetic code. fuzztran uses patterns based on the format of pattern used…

fuzzpro
Desktop

fuzzpro

Searches for patterns in protein sequences. Fuzzpro selects the optimum…

Searches for patterns in protein sequences. Fuzzpro selects the optimum searching algorithm to use, depending on the complexity of the search pattern specified. It also searches for a specified…

Information

By using OMICtools you acknowledge that you have read and accepted the terms of the end user license agreement.