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Sequence homology search software tools | Protein comparison analysis

Sequence-based protein function and structure prediction depends crucially on sequence-search sensitivity and accuracy of the resulting sequence alignments.Source text:(Remmert et al., 2011) HHblits: lightning-fast iterative protein sequence…
BLAST
Web
Desktop

BLAST Basic Local Alignment Search Tool

Allows to align query sequences against those present in a selected target…

Allows to align query sequences against those present in a selected target database. BLAST is a suite of programs, provided by NCBI, which can be used to quickly search a sequence database for…

ProtDec-LTR
Web

ProtDec-LTR

Permits to detect remote homology protein. ProtDec-LTR integrates the…

Permits to detect remote homology protein. ProtDec-LTR integrates the evolutionary information from pseudo protein representations. It facilitates the exploration of sequence and structure…

MIQS
Web

MIQS Matrix to Improve Quality in Similarity search

Identifies distantly related proteins. MIQS returns alignments for which the…

Identifies distantly related proteins. MIQS returns alignments for which the quality is well balanced between sensitivity and precision. It is based on substitution matrices generated from the…

HMMER
Desktop
Web

HMMER

Provides access to the protein homology search algorithms found in the HMMER…

Provides access to the protein homology search algorithms found in the HMMER software suite. Since the first release of the website in 2011, the search repertoire has been expanded to include the…

BLASTP
Web

BLASTP Standard Protein BLAST

Programs search protein databases using a protein query. Algorithms: blastp,…

Programs search protein databases using a protein query. Algorithms: blastp, psi-blast, phi-blast, delta-blast.

PSI-Search
Web
Desktop

PSI-Search

Identifies distantly related protein sequences. PSI-search substitutes a…

Identifies distantly related protein sequences. PSI-search substitutes a rigorous local alignment search strategy to produce optimal local alignment scores from the profile position-specific score…

PMD
Dataset

PMD Protein Mutant Database

Provides a compilation of protein mutant data, providing information on…

Provides a compilation of protein mutant data, providing information on functional and/or structural influences brought about by amino acid mutations at specific positions of a protein. PMD is an…

PyMod
Desktop

PyMod

Acts as simple and intuitive interface between PyMOL and several bioinformatics…

Acts as simple and intuitive interface between PyMOL and several bioinformatics tools (i.e., PSI-BLAST, Clustal Omega, MUSCLE, CAMPO, PSIPRED, and MODELLER). PyMod builds homology models through the…

SitEx
Dataset

SitEx

Provides projection of protein domains, functional sites and exon boundaries on…

Provides projection of protein domains, functional sites and exon boundaries on protein and coding gene sequence. SitEx concerns proteins with known 3D structure and corresponding genes. It is useful…

C-HMM
Desktop

C-HMM C-Hidden Markov Models

Identifies remote homologues from any protein sequence database. C-HMM…

Identifies remote homologues from any protein sequence database. C-HMM approach, based on hidden markov models, has been demonstrated to be powerful in identifying connections across protein domains…

Blocks Database
Dataset

Blocks Database

Collects ungapped multiple alignments of short regions. Blocks Database was…

Collects ungapped multiple alignments of short regions. Blocks Database was built from sequences of protein families using a fully automated method and allows to detect one or more of blocks…

TASSER-Lite
Web

TASSER-Lite Threading/ ASSembly/Refinement Lite

Provides a comparative modeling tool. TASSER-Lite can be apply to the…

Provides a comparative modeling tool. TASSER-Lite can be apply to the large-scale comparative modeling and is mainly developed for homologous protein sequences. The search can be run from the website…

SuperSite
Dataset

SuperSite

Offers 3D information about proteins bound compounds. SuperSite enables user to…

Offers 3D information about proteins bound compounds. SuperSite enables user to explore the relationship of ligand and receptor in atomic detail, integrating information sources about putative…

SMS
Web

SMS STING Millennium Suite

Provides a variety of algorithms and validated data, wrapped-up in a user…

Provides a variety of algorithms and validated data, wrapped-up in a user friendly web interface. STING Millennium Suite (SMS) is a new web-based suite of programs and databases providing…

SRD
Desktop

SRD Sequence Relation Drawing program

Supports the graphical visualization of results generated from sequence…

Supports the graphical visualization of results generated from sequence relationship analysis based on undirected graphs, for a wide range of either nucleic acid sequences or peptide sequences. SRD…

jackhmmer
Web

jackhmmer

Provides an iterative sequence searching to identify similarities to…

Provides an iterative sequence searching to identify similarities to functionally characterised proteins that are not detected with single sequence searching. Each iteration is compared to the…

HHsenser
Web

HHsenser

A server to offer exhaustive intermediate profile searches, which it combines…

A server to offer exhaustive intermediate profile searches, which it combines with pairwise comparison of hidden Markov models (HMM). HHsenser servers to offer exhaustive intermediate profile…

cuBLASTP
Desktop

cuBLASTP

cuBLASTP is a mapping of the BLAST algorithm onto a Graphics processing unit…

cuBLASTP is a mapping of the BLAST algorithm onto a Graphics processing unit (GPU) that uses the Compute Unified Device Architecture (CUDA) programming model.

COMA
Web
Desktop

COMA Comparison Of Multiple Alignments

Detects distant evolutionary relationship through comparison of multiple…

Detects distant evolutionary relationship through comparison of multiple protein sequence alignments. COMA is a method based on sequence profile–profile comparison. It is available under a…

CMsearch
Desktop

CMsearch

Explores simultaneously protein sequence space and protein structure space by…

Explores simultaneously protein sequence space and protein structure space by cross-modal learning. CMsearch has several advantages over existing methods: (i) instead of exploring a single space…

SparkBLAST
Desktop

SparkBLAST Spark Basic Local Alignment Search Tool

Allows to parallelize and manage the execution of BLAST either on dedicated…

Allows to parallelize and manage the execution of BLAST either on dedicated clusters or cloud environments. SparkBLAST is based on cloud computing for the provisioning of computational resources and…

3DCNN
Desktop

3DCNN 3D Convolutional Neural Network

Applies 3D convolutional neural networks for protein structural analysis. 3DCNN…

Applies 3D convolutional neural networks for protein structural analysis. 3DCNN is a framework that automatically extracts task-specific features from the raw atom distribution, driven by supervised…

PFASUM
Desktop

PFASUM PFAm SUbstitution Matrix

Allows accurate detection of homologous protein sequences and for scoring and…

Allows accurate detection of homologous protein sequences and for scoring and constructing high quality protein multiple sequence alignments (MSAs). PFASUM is based on the manually curated Pfam seed…

GeneWise
Web
Desktop

GeneWise

Predicts gene structure using similar protein sequences. GeneWise is heavily…

Predicts gene structure using similar protein sequences. GeneWise is heavily used by the Ensembl annotation system. It was developed from a principled combination of hidden Markov models (HMMs).…

PRINTS BLAST
Web

PRINTS BLAST

Provides a way to query the PRINTS database. PRINTS BLAST distils the…

Provides a way to query the PRINTS database. PRINTS BLAST distils the diagnostic essence of primary and secondary database searching into an informative. It allows rapid visual inspection of a…

FUSTr
Desktop

FUSTr Families Under Selection in Transcriptomes

Allows to detect gene families in transcriptomes under strong selection. FUSTr…

Allows to detect gene families in transcriptomes under strong selection. FUSTr provides information about candidate genes involved in the processes of adaptation, in addition to contributing to…

PHI-DAC
Dataset

PHI-DAC Protein Homology database through Dihedral Angle Conservation

Allows to find protein segments based on amino acid sequence and “Psi” and…

Allows to find protein segments based on amino acid sequence and “Psi” and “varphi” dihedral angles. PHI-DAC is a database with entry composed of four pipe delimited fields: first and second…

Peptide Match
Desktop
Web

Peptide Match

Retrieves all occurrences of a given query peptide from UniProt Knowledgebase…

Retrieves all occurrences of a given query peptide from UniProt Knowledgebase (UniProtKB) with isoforms. Peptide Match is a web application for peptide matching which also provides batch retrieval…

dissectHMMER
Web

dissectHMMER

Reproduces HMMER2/3 scores with sufficient accuracy and that it is useful in…

Reproduces HMMER2/3 scores with sufficient accuracy and that it is useful in automated decisions about homology for instructive sequence examples. DissectHMMER is a software program for dissecting…

CUDAMPF
Desktop

CUDAMPF

A hardware-aware parallel framework for accelerating computational hotspots…

A hardware-aware parallel framework for accelerating computational hotspots within the hmmsearch pipeline as well as other sequence alignment applications. CUDAMPF achieves significant speedup by…

SMPS-SS
Desktop

SMPS-SS

Allows users to analyze biological data, and especially protein data. SMPS-SS…

Allows users to analyze biological data, and especially protein data. SMPS-SS is a statistical measure that compares protein sequences by exploring the information on 'sequence space' and…

CABRA
Web

CABRA Cluster and Annotate Blast Results Algorithm

Provides a shortcut to the evaluation of a BLAST result where its clustering of…

Provides a shortcut to the evaluation of a BLAST result where its clustering of hits allows a quick classification. CABRA integrates the advantages of a BLAST search and FastaHerder clustering…

RAFTS3
Desktop

RAFTS3

A fast protein similarity search tool that utilizes a filter step for candidate…

A fast protein similarity search tool that utilizes a filter step for candidate selection based on shared k-mers and a comparison measure using a binary matrix of co-occurrence of amino acid…

ASD
Desktop

ASD Amplitude Spectrum Distance

Compares protein fragments based on the discrete Fourier transform of their Cα…

Compares protein fragments based on the discrete Fourier transform of their Cα distance matrix. ASD can be computed efficiently and provides a parameter-free measure of the global shape…

MRFalign
Desktop

MRFalign

A method for sequence-based protein homology detection that compares two…

A method for sequence-based protein homology detection that compares two protein sequences or families through alignment of two Markov random fields (MRFs), which model the multiple sequence…

blastall
Desktop

blastall

Permits users to run blast searches. blastall permits users to make searching…

Permits users to run blast searches. blastall permits users to make searching combinations to query nucleotide or peptide sequence databases for example. It is able to find similar sequences in a…

VOCS
Desktop

VOCS Viral Orthologous Clusters

Searches and extracts genome, gene and protein data from the Viral…

Searches and extracts genome, gene and protein data from the Viral Bioinformatics Resource Center (VBRC) database. VOCS includes Asfarviridae, Baculoviridae, Iridoviridae, and Poxviridae. It compares…

CS-BLAST
Desktop
Web

CS-BLAST

An extension to standard NCBI BLAST that allows to increase its sensitivity by…

An extension to standard NCBI BLAST that allows to increase its sensitivity by a factor of more than two on remote homologs at the same speed.

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…

PSimScan
Desktop

PSimScan Protein Similarity Scanner

A flexible open source protein similarity search tool which provides a…

A flexible open source protein similarity search tool which provides a significant gain in speed compared to BLASTP at the price of controlled sensitivity loss.

DELTA-BLAST
Web

DELTA-BLAST Domain Enhanced Lookup Time Accelerated BLAST

Searches a database of pre-constructed PSSMs before searching a…

Searches a database of pre-constructed PSSMs before searching a protein-sequence database, to yield better homology detection. DELTA-BLAST is a useful program for the detection of remote protein…

Afree
Desktop

Afree

Allows users to compare large-scale protein sequences. Afree is a standalone…

Allows users to compare large-scale protein sequences. Afree is a standalone software which aims to furnish a quick alternative to BLASTp by performing all-against-all sequence comparison as a single…

RACCOON
Desktop

RACCOON Relative Amino aCid COmposition in dOmains and liNkers

Allows user to compare the mean amino acid composition of a specific domain to…

Allows user to compare the mean amino acid composition of a specific domain to the mean amino acid composition of all domains, simultaneously for all available species. RACCOON is an application that…

Goanna
Web

Goanna

Allows the transfer of gene ontology (GO) annotations based on sequence…

Allows the transfer of gene ontology (GO) annotations based on sequence homology to researchers’ own data. Goanna accepts as input some protein accessions and a list of either nucleotide or protein…

Seqcksum
Web

Seqcksum Sequence checksum calculator

Creates checksums for sequences. Seqcksum concerns CRC32, CRC64-ISO,…

Creates checksums for sequences. Seqcksum concerns CRC32, CRC64-ISO, CRC64-ECMA-182, CRC32-CRC64, MD5, SHA1, SHA2 224-bit, SHA2 256-bit, SHA2 384-bit and SHA2 512-bit.

HMMER hmmscan
Web

HMMER hmmscan

Permit to search sequences against collections of profiles. HMMER hmmscan is a…

Permit to search sequences against collections of profiles. HMMER hmmscan is a web application. This tool is a simple multiple steps process: (i) user sets the tool input (e.g. sequences,…

FASTM
Web

FASTM

Makes comparisons between an inputted protein and a protein sequence database.…

Makes comparisons between an inputted protein and a protein sequence database. FASTM permits to avoid issues with low complexity sequences where matches are found due to composition rather than…

DCBLAST
Desktop

DCBLAST

Performs run on grid system with query splicing which can run National Center…

Performs run on grid system with query splicing which can run National Center for Biotechnology Information (NCBI) BLASTBLAST search comparisons. DCBLAST uses BLAST job that dramatically accelerates…

MetaDomain
Desktop

MetaDomain

Provides a protein domain classification for short reads generated by…

Provides a protein domain classification for short reads generated by next-generation sequencing technologies. MetaDomain uses relaxed position-specific score thresholds to align more reads to a…

HHblits
Web

HHblits HMM-HMM-based lightning-fast iterative sequence search

Searches for protein sequence by hidden Markov model (HMM)-HMM alignment.…

Searches for protein sequence by hidden Markov model (HMM)-HMM alignment. HHblits is a protein sequence search tool that extends HHsearch.

SitesBase
Dataset

SitesBase

Provides data about protein-ligand binding sites. SitesBase contains…

Provides data about protein-ligand binding sites. SitesBase contains pre-calculated all-against-all binding site similarities which can be used for rapid retrieval and examination of other binding…

DAhunter
Web

DAhunter

Detects homologous proteins thanks to domain architecture comparison. DAhunter…

Detects homologous proteins thanks to domain architecture comparison. DAhunter confront the query domain architecture against candidate domain architectures in the database regarding the content,…

dRHP-PseRA
Web

dRHP-PseRA

Allows users to detect remote homology proteins. dRHP-PseRA is based on…

Allows users to detect remote homology proteins. dRHP-PseRA is based on profile-based pseudo protein sequence formulation derived from protein profile. It combines four state-of-the-art predictors…

GeneSpeed
Dataset

GeneSpeed

Provides an extensive homology compilation of all protein domains within the…

Provides an extensive homology compilation of all protein domains within the transcriptomes of human, mouse, worm and fly. GeneSpeed is an online database with a free personal account. Registered…

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…

PARALIGN
Web
Desktop

PARALIGN

Uses for the identification of distantly related sequences in both nucleotide…

Uses for the identification of distantly related sequences in both nucleotide and amino acid sequence databases. PARALIGN is a rapid and sensitive similarity search tool designed to run efficiently…

ApicoAlign
Web

ApicoAlign

Finds orthologs and aligns apicomplexan proteins using a novel series of…

Finds orthologs and aligns apicomplexan proteins using a novel series of matrices. ApicoAlign can be used for five applications (1) Search Database (2) Search a genome (3) Reciprocal Hit (4) Best…

GSA
Desktop

GSA GPU-accelerated structure similarity algorithm

Speeds the performance of structure similarity search for over two orders of…

Speeds the performance of structure similarity search for over two orders of magnitude faster. GSA is a GPU-accelerated structure similarity algorithm based on atom center fragment (ACF) approach.…

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