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Protein function prediction software tools | Sequence analysis

Protein function is a concept that can have different interpretations in different biological contexts. Generally, it describes biochemical, cellular, and phenotypic aspects of the molecular events that involve the protein, including how they…
PANNZER
Desktop

PANNZER Protein ANNotation with Z-score

A high-throughput tool for more reliable functional annotation. PANNZER…

A high-throughput tool for more reliable functional annotation. PANNZER predicts Gene Ontology (GO) classes and free text descriptions about protein functionality. It uses weighted k-nearest…

SIMBAL
Desktop

SIMBAL SIMBAL

Allows for follow-up investigation in silico once correlations have been noted…

Allows for follow-up investigation in silico once correlations have been noted between pairs of protein families. SIMBAL uses clues from genomic context, such as co-occurrence or conserved gene…

SIFTS
Desktop

SIFTS Structure integration with function taxonomy and sequence

Includes cross-references to other biological resources such as Pfam, SCOP,…

Includes cross-references to other biological resources such as Pfam, SCOP, CATH, GO, InterPro and the NCBI taxonomy database. The Structure Integration with Function, Taxonomy and Sequences resource…

FunTree
Dataset

FunTree

A resource that brings together protein sequence, structure and functional…

A resource that brings together protein sequence, structure and functional information, including overall chemical reaction and mechanistic data, for structurally defined domain superfamilies.…

COMBREX-DB
Dataset

COMBREX-DB COMputational BRidges to EXperiments DataBase

Provides information about experimentally determined protein function,…

Provides information about experimentally determined protein function, relationships among proteins of unknown function and various types of experimental data. COMBREX-DB contains information on…

SVD-Phy
Desktop

SVD-Phy

A phylogenetic profiling algorithm which uses truncated singular value…

A phylogenetic profiling algorithm which uses truncated singular value decomposition to address the problem of uninformative profiles giving rise to false positive predictions. Benchmarking the…

Hotpep
Desktop

Hotpep

Performs annotation of carbohydrate-active enzymes and allows prediction of the…

Performs annotation of carbohydrate-active enzymes and allows prediction of the enzymatic activity of the proteins. Hotpep (Homology to Peptide Pattern) is a state-of-the-art method for automatic…

SIFTER
Desktop
Web

SIFTER Statistical Inference of Function Through Evolutionary Relationships

A user-friendly web interface for accurate protein function prediction using…

A user-friendly web interface for accurate protein function prediction using the SIFTER algorithm. SIFTER is a state-of-the-art sequence-based gene molecular function prediction algorithm that uses a…

ClanTox
Web

ClanTox Classifier of Animal Toxins

Serves for the extraction of sequence-driven features from the primary protein…

Serves for the extraction of sequence-driven features from the primary protein sequence followed by the application of a classification system trained on known animal toxins. ClanTox is a systematic…

Argot
Web

Argot Annotation Retrieval of Gene Ontology Terms

Allows to predict protein function. The Argot strategy treats the grouping of…

Allows to predict protein function. The Argot strategy treats the grouping of Gene Ontology (GO) terms by means of semantic similarity in order to infer protein function. Compared to the previous…

ProtFun
Web

ProtFun

Predicts protein function for a subset of classes from the Gene Ontology (GO)…

Predicts protein function for a subset of classes from the Gene Ontology (GO) classification scheme. ProtFun is optimised for computational screening of the human genome (and possibly other…

AptRank
Desktop

AptRank

Utilizes an adaptive diffusion mechanism to improve the performance of…

Utilizes an adaptive diffusion mechanism to improve the performance of BirgRank. AptRank introduces an adaptive mechanism to the PageRank framework that computes an optimal set of weights for the…

FFAS
Web
Desktop

FFAS Fold and Function Assignment System

Detects homology. FFAS includes adding optimized structural features…

Detects homology. FFAS includes adding optimized structural features (experimental or predicted), ‘symmetrical’ Z-score calculation and re-ranking the templates with a neural network. It has high…

ProtIdent
Web

ProtIdent PROTease IDENTifier

Identifies proteases and their types from a protein sequence. ProtIdent fuses…

Identifies proteases and their types from a protein sequence. ProtIdent fuses functional domain and sequential evolution information to proceed. It follows two layers, the first one to identify a…

MATEPred
Web

MATEPred Multidrug And Toxin Extrusion proteins PREDiction

Identifies Multidrug And Toxin Extrusion (MATE) proteins. MATEPred is based on…

Identifies Multidrug And Toxin Extrusion (MATE) proteins. MATEPred is based on Position Specific Scoring Matrix (PSSM) and uses Support Vector Machine (SVM). It returns sequence number, score and…

INGA
Web

INGA Interaction Network GO Annotator

A web server developed to predict protein function from a combination of three…

A web server developed to predict protein function from a combination of three orthogonal approaches. Sequence similarity and domain architecture searches are combined with protein-protein…

ProtPhylo
Web

ProtPhylo

A web-based tool to identify proteins that are functionally linked to either a…

A web-based tool to identify proteins that are functionally linked to either a phenotype or a protein of interest based on co-evolution. ProtPhylo infers functional associations by comparing protein…

PATBox
Web

PATBox

A resource which aims to aid researchers by giving them access to easy-to-use,…

A resource which aims to aid researchers by giving them access to easy-to-use, efficient and up-to-date computational tools for the prediction of the subtype of P-Type ATPase sequences. PATBox is an…

BacHbpred
Web

BacHbpred

Predicts the corresponding hemoglobin-like (HbL) subclass/family protein for a…

Predicts the corresponding hemoglobin-like (HbL) subclass/family protein for a given amino acid sequence. BacHbpred is based on support vector machines (SVM) modules. It uses amino acid composition…

NegGOA
Desktop

NegGOA Negative GO Annotations

Selects negative examples of GO annotations using ontology structure. NegGOA…

Selects negative examples of GO annotations using ontology structure. NegGOA takes advantage of the ontology structure, available annotations and potentiality of additional annotations of a protein…

UniProt-DAAC
Desktop

UniProt-DAAC UniProt Domain Architecture Alignment and Classification

A method for the automatic annotation of protein sequences in the UniProt…

A method for the automatic annotation of protein sequences in the UniProt Knowledgebase (UniProtKB) by comparing their domain architectures, classifying proteins based on the similarities and…

eccCL
Desktop

eccCL

Allows users to classify more than 25,000 instances per second. eccCL can…

Allows users to classify more than 25,000 instances per second. eccCL can accelerate the classification process in high-throughput experiments. One of the purpose of this tool is to improve…

ERI
Desktop

ERI Early Response Index

Detects disease correlated features for early diagnostic biomarker discovery.…

Detects disease correlated features for early diagnostic biomarker discovery. ERI quantifies how much classification accuracy improvement a feature can provide when it is combined with other features…

VirulentPred
Web

VirulentPred

Serves as a bacterial virulent protein prediction method which is based on…

Serves as a bacterial virulent protein prediction method which is based on bi-layer cascade Support Vector Machine (SVM). VirulentPred works with different individual protein sequence features like…

SIMAP
Dataset

SIMAP Similarity Matrix of Proteins

A database containing the similarity space formed by about all amino-acid…

A database containing the similarity space formed by about all amino-acid sequences from public databases and completely sequenced genomes. SIMAP provides pre-calculated sequence similarities…

iNR-PhysChem
Web

iNR-PhysChem

Identifies an uncharacterized protein as nuclear receptor (NR) or non-NR…

Identifies an uncharacterized protein as nuclear receptor (NR) or non-NR according to its sequences information alone. iNR-PhysChem is a web-server and a two-level predictor. A step-by-step guide is…

PUFAS
Web

PUFAS PUFs Annotation Server

A web server that predicts the possible function of an input sequence, based…

A web server that predicts the possible function of an input sequence, based upon the predicted domains and protein fold. The aim of the PUFAS server is to help identify the likely unknown function…

PSIONplus
Desktop

PSIONplus Predictor from Sequence of ION channels plus BLAST

Predicts ion channels proteins and their types, and subtypes of the…

Predicts ion channels proteins and their types, and subtypes of the voltage-gated ion channels. Empirical results show that combination of results generated by SVM model with the alignment by BLAST…

DeepSeq
Desktop

DeepSeq

Takes sequence of a protein as input and accurately predicts its functions…

Takes sequence of a protein as input and accurately predicts its functions without relying on any supporting information. DeepSeq is a novel deep learning architecture which is able to automatically…

MLDA
Desktop

MLDA Multi-label Linear Discriminant Analysis

Detects function prediction in yeast proteins. MLDA uses sequence data from…

Detects function prediction in yeast proteins. MLDA uses sequence data from GenBank and network data form BioGRID. This tool was developed to deal with multi-label classification problems and…

GROOLS
Desktop

GROOLS Genomic Rule Object-Oriented Logic System

Assists biocurators in functional annotation of proteins. GROOLS is an expert…

Assists biocurators in functional annotation of proteins. GROOLS is an expert system using paraconsistent logic that evaluates the completeness and the consistency of predicted functions through…

ProFET
Desktop

ProFET Protein Feature Engineering Toolkit

Allows easy, universal discovery of new target proteins, as well as…

Allows easy, universal discovery of new target proteins, as well as understanding the features underlying different high-level protein functions. ProFET extracts hundreds of features covering the…

EzyPred
Web

EzyPred

Predicts enzyme functional classes and subclasses. EzyPred operates by fusing…

Predicts enzyme functional classes and subclasses. EzyPred operates by fusing the Functional Domain (FunD) approach and Pseudo Position-Specific Scoring Matrix (Pse-PSSM) approach. It first…

COFACTOR
Desktop
Web

COFACTOR

A structure-based method for biological function annotation of protein…

A structure-based method for biological function annotation of protein molecules. To use COFACTOR, user needs to provide a 3D-structural model of the protein of interest. COFACTOR will thread the…

ArchaeaFun
Web

ArchaeaFun

Detects and classifies enzymes from sequence alone. ArchaeaFun finds…

Detects and classifies enzymes from sequence alone. ArchaeaFun finds information on various post-translational and localizational aspects of the protein by querying feature prediction. This…

BLProt
Desktop

BLProt

Allows the prediction bioluminescence from a protein sequence. BLProt uses a…

Allows the prediction bioluminescence from a protein sequence. BLProt uses a Support Vector Machine (SVM) which is based on physicochemical properties in order to work on bioluminescent proteins.…

SPRED
Desktop

SPRED

Identifies secretory proteins from protein sequences irrespective of N-terminal…

Identifies secretory proteins from protein sequences irrespective of N-terminal signal peptides. SPRED is a random forest method and a machine learning approach that allows correct classification of…

GASVM
Desktop

GASVM Genetic Algorithm Support Vector Machine

Predicts apoptotic protein sequences using sequences derived properties like…

Predicts apoptotic protein sequences using sequences derived properties like frequency of amino acid groups, secondary structure, and physicochemical properties. GASVM is a hybrid algorithm approach…

CombFunc
Web

CombFunc

An automated method for the prediction of protein function. CombFunc…

An automated method for the prediction of protein function. CombFunc incorporates ConFunc, a function prediction method, with other approaches for function prediction that use protein sequence, gene…

GPCRpred
Desktop
Web

GPCRpred

A support vector machine (SVM)-based method has been developed for predicting…

A support vector machine (SVM)-based method has been developed for predicting families and subfamilies of GPCRs from the dipeptide composition of proteins. The method classified GPCRs and non-GPCRs…

Pretata
Web
Desktop

Pretata

Identifies TATA-binding proteins (TBP). Pretata uses computational intelligence…

Identifies TATA-binding proteins (TBP). Pretata uses computational intelligence strategies such as Support Machine Vector (SVM). It combines physicochemical properties and secondary structure…

CleavePred
Web

CleavePred

A web tool for predicting the cleavage sites of proproteins such as prohormones…

A web tool for predicting the cleavage sites of proproteins such as prohormones and neuropeptides. CleavePred's algorithm is powered by ASAP, a Machine-Learning framework for predicting local…

BASID2CS
Dataset

BASID2CS BASID2CS: The basidiomycetes Two Componen Systems repository

A pipeline web server that extends the analysis to the complete genome…

A pipeline web server that extends the analysis to the complete genome sequences of basidiomycetes. BASID2CS has been specifically designed for the identification, classification and functional…

PILL
Desktop

PILL Predict protein functions using Incomplete hierarchical LabeLs

An algorithm to predict protein functions using incomplete hierarchical labeLs.…

An algorithm to predict protein functions using incomplete hierarchical labeLs. PILL takes into account the hierarchical and the flat taxonomy similarity between function labels, and defines a…

NRProF
Algorithm

NRProF

An automated protein functional assignment method based on the neural response…

An automated protein functional assignment method based on the neural response algorithm, which simulates the neuronal behavior of the visual cortex in the human brain. NRProF is the first instance…

Protannotator
Dataset

Protannotator

Functional annotation of protein aims to extend the knowledgebase of existing,…

Functional annotation of protein aims to extend the knowledgebase of existing, novel or relatively less studied proteins by using a number of computational techniques. Existing knowledgebase of…

WebFeature
Desktop
Web

WebFeature

An advanced version of the protein function annotation system FEATURE, which…

An advanced version of the protein function annotation system FEATURE, which achieved 99% precision and average recall of 95% across 20 representative functional sites. Web Feature evaluates the…

SCMBLP
Desktop
Web

SCMBLP

An approach to estimating the propensity scores of 400 dipeptides and 20 amino…

An approach to estimating the propensity scores of 400 dipeptides and 20 amino acids in order to design two prediction methods and characterize bioluminescent proteins (BLPs) based on a scoring card…

ProMK
Desktop

ProMK Predicting Protein Function using Multiple Kernels

Iteratively optimizes the phases of learning optimal weights and reduces the…

Iteratively optimizes the phases of learning optimal weights and reduces the empirical loss of multi-label classifier for each of the labels simultaneously. ProMK can integrate kernels selectively…

CascadeDetect
Desktop

CascadeDetect

Extracts localized features from sequence sets. CascadeDetect computes expected…

Extracts localized features from sequence sets. CascadeDetect computes expected feature counts, screens artifacts and identifies statistically significant localized features of all orders in sets of…

ETAscape
Desktop

ETAscape

Extends an existing suite of protein function annotation tools to infer…

Extends an existing suite of protein function annotation tools to infer functional residues, identify functional sites and predict protein function. ETAscape pairs state-of-the-art network analysis…

AnaGram
Web

AnaGram

A web application for protein function assignment based on identity detection…

A web application for protein function assignment based on identity detection of small significant fragments (protomotifs) that can act as modular pieces in peptide construction. The system is able…

SCI-PHY
Desktop

SCI-PHY Subfamily Classification In PHYlogenomics

A pipeline for automatic subfamily identification, followed by subfamily hidden…

A pipeline for automatic subfamily identification, followed by subfamily hidden Markov model (HMM) construction. A simple and computationally efficient scoring scheme using family and subfamily HMMs…

MitPred
Desktop
Web

MitPred

A web-server specifically trained to predict the proteins which are destined to…

A web-server specifically trained to predict the proteins which are destined to localize in mitochondria in yeast and animals particularly. The prediction is made on basis of either occurrence of…

NRpred
Desktop
Web

NRpred

A SVM based tool for the classification of nuclear receptors on the basis of…

A SVM based tool for the classification of nuclear receptors on the basis of amino acid composition or dipeptide composition. The overall prediction accuracy of amino acid composition and dipeptide…

CyclinPred
Web

CyclinPred

A SVM based prediction method to identify novel cyclins using various features…

A SVM based prediction method to identify novel cyclins using various features of proteins. CyclinPred can predict both groups of cyclins: G1/S cyclins and G2/M cyclins.

ProPhylo
Desktop

ProPhylo

A software package for high-performance phylogenetic profile searches on…

A software package for high-performance phylogenetic profile searches on desktop computers. The package implements partial phylogenetic profiling (PPP) and double partial phylogenetic profiling…

BLANNOTATOR
Desktop
Web

BLANNOTATOR

An accurate method for bacterial protein function prediction. BLANNOTATOR is…

An accurate method for bacterial protein function prediction. BLANNOTATOR is practical for genome-scale data and does not require pre-existing sequence clustering; thus, this method suits the needs…

LGEpred
Web

LGEpred

There is a correlation between gene expression and amino acid composition that…

There is a correlation between gene expression and amino acid composition that can be used to predict the expression level of genes up to a certain extent. A web server has been developed for…

CancerPred
Web

CancerPred

A web-server specially trained for predicting the Cancerlectins. CancerPred is…

A web-server specially trained for predicting the Cancerlectins. CancerPred is mainly designed for distinguishing Cancerlectins from Non-cancer lectins. The method is based upon SVM-modules developed…

MANGO
Web

MANGO

A server for predicting functional class of a protein. It predicts function…

A server for predicting functional class of a protein. It predicts function according to GO categories. The method is developed on protein in UNIPROT database whose function have been assigned…

VICMpred
Web

VICMpred

A webserver aid in broad functional classification of proteins of bacteria into…

A webserver aid in broad functional classification of proteins of bacteria into virulence factors, information molecule, cellular process and metabolism molecule. The VICMpred server uses SVM based…

COPid
Web

COPid COmposition based Protein Identification

Assists the researchers in annotating the function of a protein from its…

Assists the researchers in annotating the function of a protein from its composition using whole or part of the protein. COPid has three modules called search, composition and analysis. The search…

DNAsize
Web

DNAsize

A web server has been developed for computing the size of DNA/protein fragments…

A web server has been developed for computing the size of DNA/protein fragments from their electrophoretic mobilities using a graphical method. This server is based on the computer program DNASIZE…

Oxypred
Web

Oxypred

A method for predicting and classifying oxygen-binding proteins. Firstly,…

A method for predicting and classifying oxygen-binding proteins. Firstly, support vector machine (SVM) modules were developed using amino acid composition and dipeptide composition for predicting…

VGIchan
Web

VGIchan

Voltage-gated ion channels are integral membrane proteins that enable the…

Voltage-gated ion channels are integral membrane proteins that enable the passage of selected inorganic ions across cell membranes. VGIchan predicts voltage gated ion channels and classify them into…

PredBLP
Web

PredBLP Prediction of BioLuminescent Proteins

Allows to predict bioluminescent proteins. PredBLP generates an email to users…

Allows to predict bioluminescent proteins. PredBLP generates an email to users containing numeric score for each protein present in the latest submission. Each putative annotation appearing on the…

Lypred
Web

Lypred

Identifies Bacterial Cell Wall Lyase via pseudo amino acid composition. Lypred…

Identifies Bacterial Cell Wall Lyase via pseudo amino acid composition. Lypred can be a powerful and useful tool for the experimental study of bacterial cell wall lyase. An improved pseudo amino acid…

iHSP-PseRAAAC
Web

iHSP-PseRAAAC

Identifies the heat shock protein (HSP) families using pseudo reduced amino…

Identifies the heat shock protein (HSP) families using pseudo reduced amino acid alphabet composition. iHSP-PseRAAAC is a web-server and a predictor developed by incorporating the amino acid data…

AodPred
Web

AodPred

A support vector machine-based predictor was developed for identifying…

A support vector machine-based predictor was developed for identifying antioxidant proteins. In this predictor, the sequence was formulated by using the optimal 3-gap dipeptides obtained by using…

BLPre
Web

BLPre

Predicts bioluminescent proteins which uses a model based on auto covariance…

Predicts bioluminescent proteins which uses a model based on auto covariance and position specific scoring matrix. BLPre includes prediction features which allow users to discover many still unknown…

ThermoPred
Web

ThermoPred

Identifies thermophilic proteins based on the sequence information. ThermoPred…

Identifies thermophilic proteins based on the sequence information. ThermoPred is a web server and a support vector machine (SVM) based method to predict thermophilic proteins using the information…

CaLecPred
Web

CaLecPred

A sequence-based method to discriminate between cancerlectins and…

A sequence-based method to discriminate between cancerlectins and non-cancerlectins. The analysis of variance (ANOVA) was used to choose the optimal feature set derived from the g-gap dipeptide…

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