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Protein annotation software tools | Sequence analysis

The last decade has seen a remarkable growth in protein databases. This growth comes at a price: a growing number of submitted protein sequences lack functional annotation. Approximately 32% of sequences submitted to the most comprehensive protein…
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…

PSI-MOD
Desktop
Web

PSI-MOD

An ontology, a hierarchical controlled vocabulary forming a directed acyclic…

An ontology, a hierarchical controlled vocabulary forming a directed acyclic graph consisting of terms and definitions for protein chemical modifications, the nodes, logically linked by specific…

GPCRHMM
Web
Desktop

GPCRHMM G Protein-Coupled Receptors by Hidden Markov Model

Allows user to visualize protein sequence features. GPCRHMM offers several…

Allows user to visualize protein sequence features. GPCRHMM offers several advantages: users can zoom in on a region and zoom-dependent sequence rendering displays residues automatically at a…

PNU
Dataset

PNU Protein Naming Utility

Stores and applies customizable sets of naming rules to correct and standardize…

Stores and applies customizable sets of naming rules to correct and standardize gene and protein names within an annotated genome or metagenome. PNU is a web-based database that allows users to…

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…

UniProt-GOA
Dataset

UniProt-GOA

Provides Gene Ontology (GO) annotations to proteins in the UniProt…

Provides Gene Ontology (GO) annotations to proteins in the UniProt Knowledgebase. GOA is a database derived from both automatic predictions and manual curation methods. GO annotation dataset supplies…

RabDB
Dataset

RabDB

Displays Rab annotation for all genomes available as a part of Superfamily…

Displays Rab annotation for all genomes available as a part of Superfamily 1.75. RabDB a database created to explore the universe of the Rab family of small GTPases, key regulators of the Eukaryotic…

Rabifier
Web
Desktop

Rabifier

An automated bioinformatic pipeline for prediction and classification of Rab…

An automated bioinformatic pipeline for prediction and classification of Rab GTPases. Rabifier2 is a major update over the pipeline originally developed to identify Rab GTPases and classify them into…

FunFHMMer
Web

FunFHMMer

Provides Gene Ontology (GO) annotations for query protein sequences based on…

Provides Gene Ontology (GO) annotations for query protein sequences based on the functional classification of the domain-based CATH-Gene3D resource. FunFHMMer also provides valuable information for…

PRO
Web

PRO Protein Ontology

An ontological representation of protein-related entities. PRO defines and…

An ontological representation of protein-related entities. PRO defines and describes taxon-specific and taxon-neutral protein-related entities in three major areas: proteins related by evolution;…

Alga-PrAS
Dataset

Alga-PrAS Algal Protein Annotation Suite

Provides physicochemical, structural and functional annotations of algal…

Provides physicochemical, structural and functional annotations of algal proteome data. Alga-PrAS includes whole protein sequences of 31 algae, such as green algae, red algae, glaucophyte, oomycetes,…

RESID
Dataset

RESID

Stores annotations and structures for protein pre-, co- and post-translational…

Stores annotations and structures for protein pre-, co- and post-translational modifications including amino-terminal, carboxyl-terminal and peptide chain cross-link modifications. RESID provides…

PeptideMass
Web

PeptideMass

Allows users to utilize annotated protein sequence databases for the…

Allows users to utilize annotated protein sequence databases for the understanding of Mass Spectrometry (MS) data. PeptideMass generates the theoretical peptide masses of any protein in the…

BAR
Web

BAR Bologna Annotation Resource

Detects protein structural and functional features from sequence. BAR performs…

Detects protein structural and functional features from sequence. BAR performs transfer of statistically validated annotation among sequences that enter a cluster after constraining the alignment…

DAMA
Desktop

DAMA Domain Annotation by a Multi-objective Approach

Treats protein domain architecture prediction as a multi-objective optimization…

Treats protein domain architecture prediction as a multi-objective optimization problem. By taking into account known architectural solutions, DAMA identifies them within the protein sequence and…

ANARCI
Web
Desktop

ANARCI Antigen receptor Numbering And Receptor ClassificatIon

A tool for annotating antigen receptor variable domain amino-acid sequences…

A tool for annotating antigen receptor variable domain amino-acid sequences with five commonly used numbering schemes. It can annotate sequences with the five most popular numbering schemes: Kabat,…

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…

3DBIONOTES
Web

3DBIONOTES

Allows users to automatically annotate structural models. 3DBIONOTES authorizes…

Allows users to automatically annotate structural models. 3DBIONOTES authorizes users to: (i) expose the macromolecular structure submitted or queried by users; (ii) show the biomedical and…

AGeNNT
Desktop

AGeNNT Automatically Generates refined Neighborhood NeTworks

Generates refined Genome Neighborhood Networks (rGNNs). AGeNNT can determine…

Generates refined Genome Neighborhood Networks (rGNNs). AGeNNT can determine for each cluster-node the normalized frequencies with which the different phyla contribute sequences. It discriminates…

Plant-PrAS
Dataset

Plant-PrAS Plant-Protein Annotation Suite

A database of physicochemical and structural properties, and novel functional…

A database of physicochemical and structural properties, and novel functional region in plant proteomes. Plant-PrAS database plant species are Arabidopsis, soybean, poplar, rice, moss and algae. We…

UniGOPred
Dataset

UniGOPred

Informs about proteomes. UniGOPred provides function predictions for over 500…

Informs about proteomes. UniGOPred provides function predictions for over 500 molecular function (MF), more than 2900 biological process (BP) and 400 cellular component (CC) gene ontology (GO) terms…

The Proteins…
Web

The Proteins API

Provides searching and programmatic access to protein and associated genomics…

Provides searching and programmatic access to protein and associated genomics data such as curated protein sequence positional annotations from UniProtKB, as well as mapped variation and proteomics…

svmPRAT
Desktop

svmPRAT SVM-based protein residue annotation toolkit

Allows building support vector machine (SVM) based models for annotating amino…

Allows building support vector machine (SVM) based models for annotating amino acid residues in protein sequences using user supplied features (like PSI-BLAST profiles, or PSIPred profiles). SvmPRAT…

Dintor
Desktop

Dintor

Provides a set of over 30 tools to assist researchers in the exploration of…

Provides a set of over 30 tools to assist researchers in the exploration of genomics and proteomics datasets. Dintor covers a wide range of frequently required functionalities, from gene identifier…

SIFTER-T
Desktop
Web
dcGOR
Desktop

dcGOR

An open-source R package ‘dcGOR’ provides the bioinformatics community with…

An open-source R package ‘dcGOR’ provides the bioinformatics community with the ease to analyse ontologies and protein domain annotations.The package is freely available at CRAN for easy…

DeepQA4PA
Web

DeepQA4PA Deep Question Answering for Protein Annotation

A question-answering (QA) engines for protein annotation. Our QA engine with…

A question-answering (QA) engines for protein annotation. Our QA engine with supervised macro-reading in MEDLINE achieved a top-precision ranging from 0.58 to 0.69 to answer functional proteomics…

SInCRe
Dataset

SInCRe Structural Interactome Computational Resource

An integrated database for Mycobacterium tuberculosis H37Rv (Mtb) that collates…

An integrated database for Mycobacterium tuberculosis H37Rv (Mtb) that collates information on protein sequences, domain assignments, functional annotation and 3D structural information along with…

PROFisis
Web

PROFisis

Identifies interacting residues from sequence alone. PROFisis is a…

Identifies interacting residues from sequence alone. PROFisis is a computational-method that reliably identifies interface residues from sequence could, therefore, be extremely valuable. It…

hRMN
Desktop

hRMN heterogeneous Relational Markov Network

Provides a probabilistic graphical model for large-scale automated annotation…

Provides a probabilistic graphical model for large-scale automated annotation transfer. hRMN allows users to combine several relational features to describe a wide range of relational characteristics…

BindML
Web
Desktop

BindML

Predicts protein-protein interaction (PPI) sites using phylogenetic…

Predicts protein-protein interaction (PPI) sites using phylogenetic substitution models. BindML tries to score and identify surface residues of a protein data bank (PDB) structure which exhibits…

strut
Desktop

strut

A multi-view extension to GOstruct, a structured-output framework for function…

A multi-view extension to GOstruct, a structured-output framework for function annotation of proteins. The extended framework can learn from disparate data sources, with each data source provided to…

A A A
EST-PAC
Desktop

EST-PAC

Annotates expressed sequences tag (EST). EST-PAC is adapted for laboratories…

Annotates expressed sequences tag (EST). EST-PAC is adapted for laboratories with limited bioinformatics resources and expertise. It offers a solution to implement a database system for the…

GORetriever
Web

GORetriever

Permits users to find gene ontology annotations for a set of proteins.…

Permits users to find gene ontology annotations for a set of proteins. GORetriever just needs users to input some protein accessions listed in a text file.

APAT
Desktop

APAT Automated Protein Annotation Tool

Distributes one or more sequences to assorted annotation/prediction services.…

Distributes one or more sequences to assorted annotation/prediction services. APAT is particularly useful for large batch of sequences and can be used as a meta-tool. It can produce a combination of…

PRECIS
Web

PRECIS

Constructs protein reports from sets of related SWISS-PROT entries. PRECIS…

Constructs protein reports from sets of related SWISS-PROT entries. PRECIS offers annotation placed in the context of the family to which query sequence belongs. It returns a structured report…

Pratt
Web

Pratt

Finds patterns conserved in sets of unaligned protein sequences. Pratt permits…

Finds patterns conserved in sets of unaligned protein sequences. Pratt permits to specify the kind of patterns searched, and how many sequences should match a pattern to be reported.

BioLuminate
Desktop

BioLuminate

Provides a comprehensive modeling solution for biologics. BioLuminate is a user…

Provides a comprehensive modeling solution for biologics. BioLuminate is a user interface and the kynchpin product of the Biologics Suite that is designed from the ground up, with significant user…

FeatureP
Web

FeatureP

Predicts differential annotation of protein sequence variants. FeatureP allows…

Predicts differential annotation of protein sequence variants. FeatureP allows the user to customize his/her analysis by offering a large number of predictable features. The overall goal of protein…

HMMCAS
Web

HMMCAS

Identifies Cas proteins from a set of protein sequences or a proteome. HMMCAS…

Identifies Cas proteins from a set of protein sequences or a proteome. HMMCAS allows users to find and annotate a collection of Cas protein family Hiden Markov Models (HMMs) for protein sequences or…

AnEnPi
Web

AnEnPi Analogous Enzyme Pipeline

Assists user in the identification, clustering and annotation of analogous…

Assists user in the identification, clustering and annotation of analogous enzymes. AnEnPi is a web application that contains several features simplifying its utilization in different contexts. It…

PROTAN
Desktop

PROTAN

Allows users to predict gene ontology (GO) annotations of proteins by utilizing…

Allows users to predict gene ontology (GO) annotations of proteins by utilizing a data mining method based on protein-protein interaction (PPI) data. PROTAN evaluates the probabilistic relationships…

PSAT
Web

PSAT Protein Sequence Annotation Tool

A centralized online service offering several function-based protein annotation…

A centralized online service offering several function-based protein annotation resources, and is capable of performing high-throughput protein sequence annotation and analysis. PSAT provides a…

Annotator
Desktop

Annotator

Offers a standardized method of protein selection. Annotator addresses the…

Offers a standardized method of protein selection. Annotator addresses the issue of small sample sizes inherent in liquid chromatography coupled to tandem mass spectrometry (LC-MS/MS) data by using…

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