LSCF Bioinformatics - Target/Protein

Proteins Motifs, Patterns and PSSM

open in new windowREPRO - protein repeats analysis at Amsterdam university
open in new windowMEME SUITE for discovering motifs in groups of related sequences
open in new windowPRATT tool to discover patterns that are conserved in a set of protein sequences at Expasy, or at open in new windowEBI
open in new windowELM Eukaryotic Linear Motif resource
open in new windowEPESTFIND Finds PEST motifs as potential proteolytic cleavage sites
open in new windowPATTINPROT search Looking for patterns in protein databases

open in new windowInterProScan - search a protein against InterPro databases at EBI
open in new windowScanProsite at Expasy
open in new windowPFAM Search - of PFam protein families at EMBL-EBI
open in new windowPFAM HMM search at the Venter institute
open in new windowMOtif Scan - search a protein against a library of motifs or profiles at SIb
open in new windowFingerPRINTScan scans a protein sequence against the PRINTS Protein Database
open in new windowProteinPROPHET

open in new windowPSORTB bacterial localization prediction tool
open in new windowBlast the STEPdb (of E. coli sub-cellular locations )
open in new windowPSLpred is a SVM based method, predicts 5 major subcellular localization (cytoplasm, inner-membrane, outer- membrane, extracellular, periplasm) of Gram-negative bacteria. This method includes various SVM modules based on different features of the proteins.
open in new windowCELLO subCELlular LOcalization predictive system - assigns Gram-negative proteins to the cytoplasm , inner membrane, periplasm, outer membrane or extracellular space
open in new windowLOCtree - reports predictions based on the following: 1) Nuclear localization signals found by PredictNLS, 2) Localization inferred using Prosite motifs and Pfam domains found in the protein, and 3) SWISS-PROT keywords associated with a protein. Localization is inferred in the last two cases using the entropy-based LOCkey algorithm.
open in new windowSignalP server predicts the presence and location of signal peptide cleavage sites in amino acid sequences from different organisms: Gram-positive prokaryotes, Gram-negative prokaryotes, and eukaryotes.
open in new windowPhobius - A combined Transmemebrane Topology and Signal Peptide Prediction
open in new windowSecretomeP produces ab initio predictions of non-classical i.e. not signal peptide triggered protein secretion.

open in new windowPhobius - A combined Transmemebrane Topology and Signal Peptide Prediction
open in new windowSecretomeP - Non-classical and leaderless secretion of eukaryotic proteins, at CBS
open in new windowProP predicts arginine and lysine propeptide cleavage sites in eukaryotic proteins, at CBS
open in new windowNetChop - Proteasomal cleavages (MHC ligands), at CBS
open in new windowChloroP server Chloroplast Transit Peptide Prediction
open in new windowSignalp1.1 - predict signal sequence cleavage sites, and SignalP V2.0.b2
open in new windowLOCtree predict the subcellular localization of proteins, and DNA-binding propensity for nuclear proteins, by incorporating a hierarchical ontology of localization classes modeled onto biological processing pathways

open in new windowREP search your protein for collection of repeats
open in new windowRADAR Rapid Automatic Detection and Alignment of Repeats in protein at EMBL
open in new windowT-REKs de novo detection and alignment of repeats in Proteins