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Other software tools | Protein sequence analysis

PICR
Web

PICR Protein Identifier Cross-Reference

Maps active and deprecated protein and gene identifiers, complete amino acid…

Maps active and deprecated protein and gene identifiers, complete amino acid sequences and protein subsequences to the corresponding identifiers in over 100 different databases. PICR is a web…

UniqueProt
Desktop

UniqueProt

Allows users to create data sets of protein sequences. UniqueProt algorithm is…

Allows users to create data sets of protein sequences. UniqueProt algorithm is a way to thin out some set of sequences by removing bias originating from redundancy without losing the most important…

OXID portal
Dataset

OXID portal

Quantifies the potency and selectivity of site-specific oxidations on complex…

Quantifies the potency and selectivity of site-specific oxidations on complex proteomes. OXID portal is a web portal database developed as a compendium of proteome-wide analyses. This online resource…

ENCODE…
Web

ENCODE ChIP-Seq Significance Tool

Offers a way to conduct comparative analyses from a list of gene/transcript…

Offers a way to conduct comparative analyses from a list of gene/transcript signatures. ENCODE ChIP-Seq Significance Tool identifies enriched transcription factors (TFs) in gene or transcript lists…

LUCapedia
Dataset

LUCapedia

Integrates disparate data sets related to ancient life. LUCapedia is designed…

Integrates disparate data sets related to ancient life. LUCapedia is designed for users interested in quickly collecting evidence of deep ancestry for a small number of protein families. Users can…

GenPro
Desktop

GenPro

Allows users to build personalized protein databases (PPDs) using variant calls…

Allows users to build personalized protein databases (PPDs) using variant calls from next-generation genomic sequencing (NGS) data. GenPro was applied to the study of allelic-specific protein (ASP)…

PDEXK
Web

PDEXK

Detects PD-(D/E)XK families. PDEXK is based on the binary classification of…

Detects PD-(D/E)XK families. PDEXK is based on the binary classification of profile–profile alignments using support vector machines (SVMs). It is able to make confident assignments even for…

NEBcutter
Web

NEBcutter

Analyzes DNA sequences for the presence of restriction enzyme sites in a…

Analyzes DNA sequences for the presence of restriction enzyme sites in a convenient and easy to use manner. NEBcutter consists of a set of cooperating program modules. The module that finds…

SwiftLib
Web

SwiftLib

A web-based tool for rapid optimization of degenerate codons. SwiftLib…

A web-based tool for rapid optimization of degenerate codons. SwiftLib optimizes a degenerate codon library to cover the desired set of amino acids at several positions while staying within a…

NrichD
Dataset

NrichD

A database of computationally designed protein-like sequences, augmented into…

A database of computationally designed protein-like sequences, augmented into natural sequence databases that can perform hops in protein sequence space to assist in the detection of remote…

TSpred
Web

TSpred

Enables users to rationally design Temperature sensitive (Ts) mutants for their…

Enables users to rationally design Temperature sensitive (Ts) mutants for their proteins of interest.

MBPpred
Web

MBPpred

A profile hidden Markov model based method capable of detecting membrane…

A profile hidden Markov model based method capable of detecting membrane binding proteins (MBPs) from information encoded in their amino acid sequence. MBPpred identifies MBPs that contain one or…

Quantiprot
Desktop

Quantiprot

Allows to compare two sequence sets in a 2d feature space defined by the…

Allows to compare two sequence sets in a 2d feature space defined by the quantitative properties of sequences. Quantiprot is a powerful, flexible and extensible Python package for analyzing protein…

ArchSchema
Web
Desktop

ArchSchema

Plots related Pfam domain architectures as a dynamic graph rather than as a…

Plots related Pfam domain architectures as a dynamic graph rather than as a list of matches. ArchSchema uses two strategies to focus on the most interesting part of the network whenever number of…

TFpredict
Web
Desktop

TFpredict

Identifies transcription factors (TFs), predicts their structural superclass,…

Identifies transcription factors (TFs), predicts their structural superclass, and detects their DNA-binding domains given a protein sequence of interest. TFpredict is implemented in a Java…

RepeatedHighDim
Desktop

RepeatedHighDim

Allows to conduct global tests in proteomics experiments. RepeatedHighDim is…

Allows to conduct global tests in proteomics experiments. RepeatedHighDim is based on a mixed linear model combined with a permutation procedure and missing values imputation. It is able to detect…

d-Omix
Web

d-Omix

Integrates various analyses of domain combinations into a unified and…

Integrates various analyses of domain combinations into a unified and comparative platform. d-Omix is applicable with various domain search tools. It provides five distinct sections: (1) Data tab for…

C-Terminome
Dataset

C-Terminome

Helps scientists explore the functional role of C-termini in proteins of…

Helps scientists explore the functional role of C-termini in proteins of interest. C-Terminome contains thousands of C-terminal minimotifs with known function. Functions of other C-termini can be…

CWDPRNP
Desktop

CWDPRNP Chronic Wasting Disease Prion protein gene

Allows to analyze cervid prion protein gene (PRNP) sequences. CWDPRNP is able…

Allows to analyze cervid prion protein gene (PRNP) sequences. CWDPRNP is able to identify PRNP sequence variation among individuals via multiple sequence alignment. It permits users to visualize…

OOgenesis_Pred
Desktop

OOgenesis_Pred

Predicts oogenesis proteins. OOgenesis_Pred is based on support vector machine…

Predicts oogenesis proteins. OOgenesis_Pred is based on support vector machine (SVM) and a comprehensive protein feature. It can differentiate oogenesis from non-oogenesis proteins and shows high…

NeXtProt…
Web

NeXtProt peptide uniqueness checker

Offers a web app and a corresponding application programming interface (API)…

Offers a web app and a corresponding application programming interface (API) service to define which peptide can be used to validate the existence of human proteins. NeXtProt peptide uniqueness…

ACRF
Web

ACRF

Enables the accurate prediction of residue burial states, which should greatly…

Enables the accurate prediction of residue burial states, which should greatly facilitate protein structure prediction and evaluation. ACRF is a high-order conditional random field model that…

TRITON
Desktop

TRITON

Allows for protein mutant modeling and the docking ligand molecules into them.…

Allows for protein mutant modeling and the docking ligand molecules into them. TRITON can be used to investigate mechanisms of protein–ligand interactions and to assess the role of individual…

HHalign-Kbest
Desktop
Web

HHalign-Kbest

A web application for optimized model generation through sub optimal HMM-HMM…

A web application for optimized model generation through sub optimal HMM-HMM sequence alignment. HHalign-KBest is useful to model the structure of protein domains using automatically optimized…

NLR-parser
Desktop

NLR-parser

A tool to rapidly annotate the NLR complement from sequenced plant genomes. The…

A tool to rapidly annotate the NLR complement from sequenced plant genomes. The NLR-Parser refines the output of MAST and reliably annotates disease resistance genes encoding for nucleotide-binding…

CryGetter
Desktop

CryGetter

Aggregates Cry protein data, helping researchers of Bacillus thuringiensis and…

Aggregates Cry protein data, helping researchers of Bacillus thuringiensis and its Crystal proteins to deal with this data and allowing them to get all the relevant information for their work in a…

RedHom
Web

RedHom

Finds a subset with low sequence similarity. RedHom uses as input an amino acid…

Finds a subset with low sequence similarity. RedHom uses as input an amino acid sequence.

DETECTER
Desktop
Leaf
Desktop

Leaf

Allows discovery of maximum independent sets. Leaf was applied to generate…

Allows discovery of maximum independent sets. Leaf was applied to generate non-redundant sets from the PDB, using various sequence similarity and structure quality parameters, and several genomes. It…

A Syllabus of…
Dataset

A Syllabus of Human Hemoglobin Variants

Provides information about known human Hb variants. A Syllabus of Human…

Provides information about known human Hb variants. A Syllabus of Human Hemoglobin Variants contains more than 600 Hb variants. This resource is useful for researchers wishing to better understand…

PRIAM
Web
Desktop

PRIAM PRofils pour l’Identification Automatisée du Métabolisme

Detects automatically enzyme in a fully sequenced genome, based on the…

Detects automatically enzyme in a fully sequenced genome, based on the classification of enzymes in the ENZYME database. PRIAM relies on sets of position-specific scoring matrices automatically…

iAFP-Ense
Web

iAFP-Ense

Predicts the Antifreeze protein. iAFP-Ense is a protector that can become a…

Predicts the Antifreeze protein. iAFP-Ense is a protector that can become a useful high-throughput software for both basic research and drug development. This random forests algorithm was adopted to…

SIBIS
Desktop

SIBIS

The prediction of protein coding genes is a major challenge that depends on the…

The prediction of protein coding genes is a major challenge that depends on the quality of genome sequencing, the accuracy of the model used to elucidate the exonic structure of the genes, and the…

SCMPSP
Desktop

SCMPSP

Predicts and characterizes photosynthetic proteins (PSPs) based on a scoring…

Predicts and characterizes photosynthetic proteins (PSPs) based on a scoring card method (SCM) from sequences. We first established a new dataset from SwissPort consisting of 649 PS proteins…

aPPRove
Desktop
Web

aPPRove

A HMM-based method for accurate prediction of RNA and pentatricopeptide repeat…

A HMM-based method for accurate prediction of RNA and pentatricopeptide repeat protein binding. aPPRove takes as input a PPR protein (primary structure), one or more RNA transcripts or binding…

RiceRBP
Dataset

RiceRBP

Contains 257 experimentally identified RNA binding proteins (RBPs). For each of…

Contains 257 experimentally identified RNA binding proteins (RBPs). For each of the identified proteins, RiceRBP database provides information on transcript and protein sequence, predicted protein…

CyanoPhyChe
Dataset

CyanoPhyChe

Aids to choosing optimal conditions for expression, purification and…

Aids to choosing optimal conditions for expression, purification and characterization of a cyanobacterial protein. CyanoPhyChe is a collection of the calculated physicochemical properties,…

Hydrophobicity…
Desktop

Hydrophobicity Grapher

Graphs the hydrophobicity/hydrophilicity of a sequence of amino acids.…

Graphs the hydrophobicity/hydrophilicity of a sequence of amino acids. Hydrophobicity Grapher provides a sliding window whose size can be specified by the user. Several hydrophobicity scales can be…

MAPanalyzer
Web

MAPanalyzer

A microtubule-associated protein (MAP)-centered online analysis tool which…

A microtubule-associated protein (MAP)-centered online analysis tool which consists of a MAP database and a MAP predictor. In the database, a core MAP dataset, which is fully manually curated from…

iMem-Seq
Web

iMem-Seq

A multi-label classifier for identifying membrane proteins with single and…

A multi-label classifier for identifying membrane proteins with single and multiple types via physical-chemical property matrix and Grey-PSSM. As a demonstration, the jackknife cross-validation was…

ProteoStats
Desktop

ProteoStats

Provides many FDR estimation and visualization features for several popular…

Provides many FDR estimation and visualization features for several popular search algorithms. ProteoStats also provides accurate q-values, which can be easily integrated in any proteomics pipeline…

Bpe
Desktop

Bpe Basic Protein Engineering

An engineering toolkit for performing basic operations on a protein structure.…

An engineering toolkit for performing basic operations on a protein structure. Bpe can be integrated as part of a pipeline for computational protein structure characterization or as a standalone…

HProtDB
Dataset

HProtDB Halophile Protein Database

A systematic attempt to document the biochemical and biophysical properties of…

A systematic attempt to document the biochemical and biophysical properties of proteins from halophilic archaea/bacteria which may be involved in adaptation of these organisms to saline conditions.…

CutProtFam-Pred
Web

CutProtFam-Pred

An on-line tool that allows one to query sequences from proteomes or translated…

An on-line tool that allows one to query sequences from proteomes or translated transcriptomes, for the accurate detection and classification of putative structural cuticular proteins.

FunCat
Dataset

FunCat Functional Catalogue

Helps for the description of proteins using a structured controlled vocabulary.…

Helps for the description of proteins using a structured controlled vocabulary. FunCat is a comprehensive and functional classification scheme for the annotation of functional genome information.…

G-Score
Web

G-Score Germinality Index Calculator

Determines the germinality of a given amino acid sequence. G-Score uses the…

Determines the germinality of a given amino acid sequence. G-Score uses the germ-line variables genes from the NCBI databases. It returns a link that redirect users to a plain text page results.

BLIMPS
Desktop

BLIMPS

Provides a blocks-based method for functional genomics.

Provides a blocks-based method for functional genomics.

Antigenic…
Web

Antigenic Peptide Prediction

Allows prediction of antigenic determinants. Antigenic Peptide Prediction is…

Allows prediction of antigenic determinants. Antigenic Peptide Prediction is based on a table that underlines the occurrence of amino acid residues in experimentally known segmental epitopes. It…

Proteax
Web
Desktop

Proteax

Permits to handle proteins that are modified or derivate. Proteax allows to…

Permits to handle proteins that are modified or derivate. Proteax allows to interact with post-translationally and chemically modified protein sequences. It facilitates the transfer of data to…

SAPS
Web

SAPS Statistical Analysis of Protein Sequences

Calculates protein sequence properties thank to statistics. SAPS can deal with…

Calculates protein sequence properties thank to statistics. SAPS can deal with compositional biases, clusters and runs of charge and other amino acid types, different kinds and extents of repetitive…

pro2nick
Web

pro2nick

Automatically name engineered proteins. pro2nick is a web application that…

Automatically name engineered proteins. pro2nick is a web application that generates nicknames for protein sequences. The software constructs the name from an amino acid sequence, using the most…

Prime
Desktop

Prime

Predicts protein structure. Prime is based on homology models and fold…

Predicts protein structure. Prime is based on homology models and fold recognition. It uses a combination of sequence and secondary structure information to calculate alignments. The tool is able to…

Amino Acid…
Desktop

Amino Acid Residue Frequency Summarizer

Reads text file or fasta file containing peptide or protein sequences and…

Reads text file or fasta file containing peptide or protein sequences and prepares statistics on the occurrence of each amino acid residue throughout the file. The Amino Acid Residue Frequency…

DIRProt
Web

DIRProt

Discriminates the insecticide resistant proteins from non-resistant proteins.…

Discriminates the insecticide resistant proteins from non-resistant proteins. DIRProt is an online prediction server developed for computational prediction of insecticide resistant proteins. Four…

HHalign
Web

HHalign

Generates an hidden Markov model (HMM) from the alignments given and calculates…

Generates an hidden Markov model (HMM) from the alignments given and calculates the optimal alignment and all significant non-overlapping suboptimal alignments. HHalign compares two alignments with…

pepwindow
Desktop

pepwindow

Draws a hydropathy plot for a protein sequence. pepwindow draws a classic Kyte…

Draws a hydropathy plot for a protein sequence. pepwindow draws a classic Kyte & Doolittle hydropathy plot for a protein sequence. It calculates hydropathy in windows of a specified size over the…

pepnet
Desktop

pepnet

Draws a helical net for a protein sequence. pepnet is a method of displaying…

Draws a helical net for a protein sequence. pepnet is a method of displaying the residues of a protein in a simple 3,4,3,4 repeating pattern that emulates at a simple level the arrangement of…

oddcomp
Desktop

oddcomp

Identifies proteins with specified sequence word composition. oddcomp reads one…

Identifies proteins with specified sequence word composition. oddcomp reads one or more protein sequences, identifies proteins containing regions with a specific sequence word composition, then…

hmoment
Desktop

hmoment

Calculates and plots hydrophobic moment for protein sequence(s). hmoment plots…

Calculates and plots hydrophobic moment for protein sequence(s). hmoment plots or writes out the hydrophobic moment calculated for overlapping windows over one or more input protein sequences. The…

octanol
Desktop

octanol

Draws a White-Wimley protein hydropathy plot. octanol draws a hydropathy plot…

Draws a White-Wimley protein hydropathy plot. octanol draws a hydropathy plot for an input protein sequence. Command line options allow the display of the octanol and interface values, or hiding the…

patmatdb
Desktop

patmatdb

Searches protein sequences with a sequence motif. patmatdb returns a standard…

Searches protein sequences with a sequence motif. patmatdb returns a standard EMBOSS report file including the number of matches between the motif and each input sequence, length of match, start and…

pepwheel
Desktop

pepwheel

Draws a helical wheel diagram for a protein sequence. pepwheel displays the…

Draws a helical wheel diagram for a protein sequence. pepwheel displays the sequence in a helical representation as if looking down the axis of the helix. It is useful for highlighting amphipathicity…

inforesidue
Desktop

inforesidue

Returns information on a given amino acid residue. inforesidue reports the…

Returns information on a given amino acid residue. inforesidue reports the defined properties for all known residues, or for any residues specified by the user. Reads the Eresidues.iub file to define…

pepstats
Desktop

pepstats

Calculates statistics of protein properties. pepstats reads one or more protein…

Calculates statistics of protein properties. pepstats reads one or more protein sequences and writes an output file with various statistics on the protein properties. This includes (i) molecular…

antigenic
Desktop

antigenic

Finds antigenic sites in proteins. Antigenic predicts potentially antigenic…

Finds antigenic sites in proteins. Antigenic predicts potentially antigenic regions of a protein sequence, using the method of Kolaskar and Tongaonkar. This method is based on a single parameter and…

patmatmotifs
Desktop

patmatmotifs

Scans a protein sequence with motifs from the PROSITE database. patmatmotifs…

Scans a protein sequence with motifs from the PROSITE database. patmatmotifs writes a standard EMBOSS report file with details of the location and score of any matching motifs. The full documentation…

Webcutter
Web

Webcutter

Helps restriction map nucleotide sequences. Webcutter is a free on-line tool…

Helps restriction map nucleotide sequences. Webcutter is a free on-line tool with a simple, customizable interface, a worldwide platform-independent accessibility, a seamless interfaces to…

multilevelPSA
Desktop

multilevelPSA Multilevel Propensity Score Analysis

Estimates and visualizes multilevel propensity score models. multilevelPSA…

Estimates and visualizes multilevel propensity score models. multilevelPSA provides cluster-based functions for estimating propensity scores as well as graphics to exhibit results for multilevel data.

Protein…
Desktop

Protein Coverage Summarizer

Determines the percent of the residues in each protein sequence that have been…

Determines the percent of the residues in each protein sequence that have been identified. Protein Coverage Summarizer requires two input files: the first should contain the protein names and protein…

Protein…
Desktop

Protein Sequence Motif Extractor

Reads a fasta file or tab delimited file containing protein sequences, then…

Reads a fasta file or tab delimited file containing protein sequences, then looks for the specified motif in each protein sequence. Protein Sequence Motif Extractor uses the /N switch to specify the…

GRAVY…
Web

GRAVY Calculator

A calculator for the grand average of hydropathy (GRAVY) value for protein…

A calculator for the grand average of hydropathy (GRAVY) value for protein sequences. The GRAVY value is defined by the sum of hydropathy values of all amino acids divided by the protein length.

IndelFR
Dataset

IndelFR Indel Flanking Region Database

Provides data regarding indels and their flanking regions within homologous…

Provides data regarding indels and their flanking regions within homologous domains. IndelFR offers sequence and structure information of more than 2 900 000 indels and their flanking regions,…

PfamAlyzer
Web

PfamAlyzer

Enables in-depth analysis of the wealth of information contained within the…

Enables in-depth analysis of the wealth of information contained within the Pfam database. PfamAlyzer integrates the majority of the features present at the Pfam database sites. It uses Drag &…

Agos
Web

Agos Argonaute-binding domain screener

Identifies de novo tryptophan–glycine and/or glycine–tryptophan (WG/GW)…

Identifies de novo tryptophan–glycine and/or glycine–tryptophan (WG/GW) Argonaute-binding domains in eukaryotic proteins. Agos provides a web server that can interpret a single protein or a DNA…

TFPP
Web

TFPP

Recognizes flagellar proteins in Trypanosma brucei. TFPP identifies a large…

Recognizes flagellar proteins in Trypanosma brucei. TFPP identifies a large number of flagellar proteins with high confidence. It is based on a support vector machine (SVM) classifier to make its…

MannDB
Dataset

MannDB

Gathers sequence analyses for complete proteomes of bacterial and viral…

Gathers sequence analyses for complete proteomes of bacterial and viral pathogens from several governmental agencies' lists of bio-threat agents. MannDB is an open source database that…

PCHM
Dataset

PCHM Proteome Comparison of Human Mitochondria

Aids in browsing, searching and accessing complete annotations of data relevant…

Aids in browsing, searching and accessing complete annotations of data relevant to each mitochondrial protein of interest. PCHM is a database that provides a variety of query algorithms for peptide…

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