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Secreted protein databases | Sequence analysis

The secretome constitutes an important class of proteins that control and regulate a multitude of biological and physiological processes, thus making it a clinically relevant source for biomarkers and therapeutic target discoveries (Hathout, 2007;…
SignalP
Web
Desktop

SignalP

Predicts the presence and location of signal peptide cleavage sites in amino…

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. SignalP is…

EV-TRACK
Dataset

EV-TRACK

Regroups extracellular vesicle (EV) biology research. EV-TRACK was constructed…

Regroups extracellular vesicle (EV) biology research. EV-TRACK was constructed in order to (1) create an informed dialog among researchers about relevant experimental parameters, (2) improve the…

TargetP
Web

TargetP

Predicts the subcellular location of eukaryotic proteins. The location…

Predicts the subcellular location of eukaryotic proteins. The location assignment is based on the predicted presence of any of the N-terminal presequences: chloroplast transit peptide (cTP),…

Phobius
Web
Desktop

Phobius

Combines transmembrane topology and signal peptide predictions. Phobius…

Combines transmembrane topology and signal peptide predictions. Phobius provides an easy and accurate mean to predict signal peptides and transmembrane topology from an amino acid sequence. Phobius…

Signal-3L
Web

Signal-3L

Predicts improved signal peptide. Signal-3L uses a hierarchical protocol that…

Predicts improved signal peptide. Signal-3L uses a hierarchical protocol that determines the existence of a signal peptide and then prioritizes potential cleavage sites. The tool uses statistical…

sigcleave
Web

sigcleave

Predicts the site of cleavage between a signal sequence and the mature exported…

Predicts the site of cleavage between a signal sequence and the mature exported protein.

WoLF PSORT
Web

WoLF PSORT

An extension of the PSORT II program for protein subcellular location…

An extension of the PSORT II program for protein subcellular location prediction. WoLF PSORT converts protein amino acid sequences into numerical localization features; based on sorting signals,…

PSORTb
Web

PSORTb

A precise bacterial localization prediction tool. You can currently submit one…

A precise bacterial localization prediction tool. You can currently submit one or more Gram-positive or Gram-negative bacterial sequences or archaeal sequences in FASTA format.

PrediSi
Web
Desktop

PrediSi Prediction of Signal peptides

Identifies signal peptides and their corresponding cleavage positions. PrediSi…

Identifies signal peptides and their corresponding cleavage positions. PrediSi is a web server that allows users to analyze whole proteome datasets. The software’s algorithm is based on a position…

FunSecKB
Dataset

FunSecKB Fungal Secretome KnowledgeBase

An improved and updated version of the fungal secretome and subcellular…

An improved and updated version of the fungal secretome and subcellular proteome, i. e. protein subcellular location, knowledgebase. The fungal protein sequence data were retrieved from UniProtKB,…

SPD
Dataset

SPD Secreted Protein Database

Based on a bioinformatic pipeline and manual check, A collection of secreted…

Based on a bioinformatic pipeline and manual check, A collection of secreted proteins has been developed from Human, Mouse and Rat proteomes, which includes sequences from SwissProt, Trembl, Ensembl…

DBSecSys
Dataset

DBSecSys Database of Burkholderia malleiSecretion Systems

A database of B. mallei secretion system proteins. The database organization…

A database of B. mallei secretion system proteins. The database organization provided capability to store and retrieve comprehensive information about pathogen proteins associated with secretion…

MEMSAT
Web

MEMSAT MEMbrane protein Structure And Topology

A program which predicts the secondary structure and topology of all-helix…

A program which predicts the secondary structure and topology of all-helix integral membrane proteins based on the recognition of topological models.

LipoP
Web

LipoP

A method to predict lipoprotein signal peptides in Gram-negative Eubacteria.

A method to predict lipoprotein signal peptides in Gram-negative Eubacteria.

SecReT4
Dataset

SecReT4

An integrated database providing comprehensive information of type IV secretion…

An integrated database providing comprehensive information of type IV secretion systems (T4SSs) in bacteria.

Signal-CF
Web

Signal-CF Signal Coupling Fusion

Identifies signal peptide sequences and their cleavage sites. Signal-CF starts…

Identifies signal peptide sequences and their cleavage sites. Signal-CF starts by identifying a query protein as secretory or non-secretory and then identifies the cleavage site of its signal…

SecretomeP
Web

SecretomeP

Produces ab initio predictions of non-classical i.e. not signal peptide…

Produces ab initio predictions of non-classical i.e. not signal peptide triggered protein secretion. The method queries a large number of other feature prediction servers to obtain information on…

PRED-TAT
Web

PRED-TAT

Prediction of twin-arginine and secretory signal peptides with Hidden Markov…

Prediction of twin-arginine and secretory signal peptides with Hidden Markov Models.

TATFIND
Web

TATFIND

Predicts the presence of prokaryotic Twin-Arginine Translocation (Tat) signal…

Predicts the presence of prokaryotic Twin-Arginine Translocation (Tat) signal peptides.

TatP
Web

TatP

Predicts the presence and location of Twin-arginine signal peptide cleavage…

Predicts the presence and location of Twin-arginine signal peptide cleavage sites in bacteria.

SPOCTOPUS
Web

SPOCTOPUS

A method for combined prediction of signal peptides and membrane protein…

A method for combined prediction of signal peptides and membrane protein topology, suitable for genome-scale studies.

VerSeDa
Dataset

VerSeDa Vertebrate Secretome Database

Accelerates the prediction process for whole secretomes (the full set of…

Accelerates the prediction process for whole secretomes (the full set of secreted proteins by a given organism). VerSeDa stores information about proteins that are predicted to be secreted from cells…

ExoCarta
Dataset

ExoCarta

A manually curated database of exosomal proteins, RNA and lipids. ExoCarta…

A manually curated database of exosomal proteins, RNA and lipids. ExoCarta catalogs information from both published and unpublished exosomal studies. The mode of exosomal purification and…

Philius
Web
Desktop

Philius

Simultaneously detects signal peptides and predicts the topology of…

Simultaneously detects signal peptides and predicts the topology of transmembrane proteins. Philius is a dynamic Bayesian network (DBN)-based approach to transmembrane protein topology prediction.…

Signal-BLAST
Web

Signal-BLAST

Predicts signal peptide by sequence alignment. Signal-BLAST is a public web…

Predicts signal peptide by sequence alignment. Signal-BLAST is a public web service.

FSD
Dataset

FSD Fungal Secretome Database

For collecting and analyzing fungal secretomes. A three-layer hierarchical…

For collecting and analyzing fungal secretomes. A three-layer hierarchical identification rule based on nine prediction programs was used to identify putative secretory proteins in 158…

EffectorP
Web
Desktop

EffectorP

A prediction program for fungal effectors based on machine learning to predict…

A prediction program for fungal effectors based on machine learning to predict fungal effectors from secretomes, which eliminates the reliance on manually set thresholds such as small size and…

PRED-LIPO
Web

PRED-LIPO

A Hidden Markov Model method for the prediction of lipoprotein signal peptides…

A Hidden Markov Model method for the prediction of lipoprotein signal peptides of Gram-positive bacteria.

PECAS
Web

PECAS Prokaryotic and Eukaryotic Classical Analysis of Secretome

A pipeline for the prediction of secreted proteins. PECAS overcomes previously…

A pipeline for the prediction of secreted proteins. PECAS overcomes previously mentioned next-generation sequencing (NGS) issues and enables potential users to carry out predictions of secreted…

LAB-Secretome
Web

LAB-Secretome

A comparative analysis of the predicted secretomes of lactic acid bacteria.

A comparative analysis of the predicted secretomes of lactic acid bacteria.

NeuroPID
Web

NeuroPID Neuropeptide Precursors Identifier

An online machine-learning tool that identifies metazoan Neuropeptide (NP)…

An online machine-learning tool that identifies metazoan Neuropeptide (NP) precursors.

SecReT6
Web

SecReT6

An integrated database providing comprehensive information on type VI secretion…

An integrated database providing comprehensive information on type VI secretion systems (T6SSs) in bacteria. SecReT6 offers a unique, readily explorable archive of known and putative T6SSs, and…

EVpedia
Dataset

EVpedia

A public database for extracellular vesicles research. This community web…

A public database for extracellular vesicles research. This community web portal contains a database of publications and vesicular components, identification of orthologous vesicular components,…

SOSUI-GramN
Web

SOSUI-GramN

A predictive software system for assessing the subcellular localization of…

A predictive software system for assessing the subcellular localization of proteins in Gram-negative bacteria.

OrysPSSP
Dataset

OrysPSSP Platform for Small Secreted Proteins

A comparative platform for small secreted proteins (SSPs) from rice and other…

A comparative platform for small secreted proteins (SSPs) from rice and other plants. OrysPSSP provides users with several flexible tools and integrates related genome resources to search, validate,…

Vesiclepedia
Dataset

Vesiclepedia

A manually curated compendium of molecular data (lipid, RNA, and protein)…

A manually curated compendium of molecular data (lipid, RNA, and protein) identified in different classes of extracellular vesicles (EVs) from more than 300 independent studies published over the…

LnSignal
Web

LnSignal Labelling N-terminal Signal peptide cleavage site

Classify proteins with or without signal peptides. LnSignal is based on a…

Classify proteins with or without signal peptides. LnSignal is based on a discriminative scoring method that integrates a hydrophobicity alignment. It can locate the highest average hydrophobicity…

MetazSecKB
Dataset

MetazSecKB

A secretome and subcellular proteome knowledgebase specifically designed for…

A secretome and subcellular proteome knowledgebase specifically designed for metazoan, i.e. human and animals. The protein sequence data, consisting of over 4 million entries with 121 species having…

HCSD
Dataset

HCSD Human Cancer Secretome Database

A comprehensive database for human cancer secretome data. The cancer secretome…

A comprehensive database for human cancer secretome data. The cancer secretome describes proteins secreted by cancer cells and structuring information about the cancer secretome will enable further…

MycoSec
Dataset

MycoSec

A comprehensive database of potential mycobacterial secretomes (MycoSec) using…

A comprehensive database of potential mycobacterial secretomes (MycoSec) using pre-existing algorithms for secretome prediction for researchers interested in this particular field. The database…

iSMP-Grey
Web

iSMP-Grey

A computational predictor that can be used to identify the secretory proteins…

A computational predictor that can be used to identify the secretory proteins of malaria parasite based on the protein sequence information alone. During the prediction process a protein sample was…

PlantSecKB
Dataset

PlantSecKB Plant Secretome and Subcellular Proteome KnowledgeBase

A database for the plant research community to access and curate plant protein…

A database for the plant research community to access and curate plant protein subcellular locations, with a focus on secreted proteins. PlantSecKB is constructed with all the available plant protein…

AtlasT4SS
Dataset

AtlasT4SS

A manual curated database that describes a large number of proteins related to…

A manual curated database that describes a large number of proteins related to the type IV secretion system reported in Gram-negative and Gram-positive bacteria, as well as in Archaea.

ProtSecKB
Dataset

ProtSecKB

A knowledgebase for protist secretomes as well as protist proteins located in…

A knowledgebase for protist secretomes as well as protist proteins located in other subcellular locations. Protein sequences are obtained from UniProtKB. Subcellular locations are identified using…

SPScan
Desktop

SPScan

Scans protein sequences for the presence of secretory signal peptides (SPs).

Scans protein sequences for the presence of secretory signal peptides (SPs).

TMHMM
Web
Desktop

TMHMM

Predicts all membrane proteins in a large collection of mostly fully sequenced…

Predicts all membrane proteins in a large collection of mostly fully sequenced genomes, and provides statistics on the frequency of proteins with different topologies. One of the main advantages of…

ProtComp
Desktop

ProtComp

A program for identification of sub-cellular localization of eukaryotic…

A program for identification of sub-cellular localization of eukaryotic proteins.

HSD
Dataset

HSD Helminth Secretome Database

A compilation excretory secretory proteins from parasitic helminths. Helminth…

A compilation excretory secretory proteins from parasitic helminths. Helminth Secretome Database serves as a repository for ES proteins predicted using classical and non-classical secretory pathways,…

YPD
Dataset

YPD Yeast Protein Database

The Yeast Protein Database (YPD) is a curated database for the proteome of…

The Yeast Protein Database (YPD) is a curated database for the proteome of Saccharomyces cerevisiae. It consists of ∼6000 Yeast Protein Reports, one for each of the known or predicted yeast…

SecretP
Web

SecretP

A method for predicting mammalian secreted proteins. SecretP is able to…

A method for predicting mammalian secreted proteins. SecretP is able to distinguish classically secreted proteins (CSPs), non-classically secreted proteins (NCSPs) and non-secreted proteins (NSPs) in…

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