Identifying sequences (in a target database) having statistically significant local alignments with a given query is routine in computational biology. Source text: Chen et al., 2015.
Curator: Vincent Ranwez

Web app
Translated BLAST:… Translated BLAST: tblastn

TBLASTN Translated BLAST: tblastn

Identifies database sequences encoding proteins similar to the query. tblastn…

Identifies database sequences encoding proteins similar to the query. tblastn consists of sequences from databases in the International Nucleotide Sequence Database Collaboration and RefSeq sequences…

Web app
WU-BLAST WU-BLAST

WU-BLAST

The emphasis of this tool is to find regions of sequence similarity quickly,…

The emphasis of this tool is to find regions of sequence similarity quickly, with minimum loss of sensitivity.

Web app
FASTA FASTA

FASTA

This tool provides sequence similarity searching against protein databases…

This tool provides sequence similarity searching against protein databases using the FASTA suite of programs.

Web app
Translated BLAST:… Translated BLAST: tblastx

TBLASTX Translated BLAST: tblastx

Search translated nucleotide database using a translated nucleotide query.

Search translated nucleotide database using a translated nucleotide query.

Web app
Standard Nucleotide… Standard Nucleotide BLAST

BLASTN Standard Nucleotide BLAST

Programs search nucleotide databases using a nucleotide query. Algorithms:…

Programs search nucleotide databases using a nucleotide query. Algorithms: blastn, megablast, discontiguous megablast.

Web app
Standard Protein BLAST Standard Protein BLAST

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.

Web app
ENA Sequence Search ENA Sequence Search

ENA Sequence Search

EMBL-EBI has a nucleotide search tool which is far faster than BLAST for large…

EMBL-EBI has a nucleotide search tool which is far faster than BLAST for large datasets, with only a marginal loss in search sensitivity.

Desktop app
TreeSeq TreeSeq

TreeSeq

A software tool with a quaternary tree search structure for the analysis of…

A software tool with a quaternary tree search structure for the analysis of sequence data. This permits rapid searches for sequences of interest in large datasets. This is a terminal based version of…

Desktop app
PatMaN PatMaN

PatMaN

Searches for short patterns in large DNA databases, allowing for approximate…

Searches for short patterns in large DNA databases, allowing for approximate matches.

Desktop app
Graphics Processing… Graphics Processing Unit - Basic Local Alignment…

GPU-BLAST Graphics Processing Unit - Basic Local Alignment Search Tool

A package to execute BLAST (Basic Local Alignment Search Tool). GPU-BLAST…

A package to execute BLAST (Basic Local Alignment Search Tool). GPU-BLAST aligns query sequences against those present in a selected target database. This software can realize protein alignment…

Desktop app
Smith-Waterman… Smith-Waterman database searches with…
Desktop app
ScalaBlast ScalaBlast

ScalaBlast

Parallelizes the BLAST calculations by dynamically scheduling them across…

Parallelizes the BLAST calculations by dynamically scheduling them across processors using a fault-resilient scheme. ScalaBLAST is designed to run a large number of queries against either large or…

Desktop app
MultiGeneBlast MultiGeneBlast

MultiGeneBlast

Performs homology searches with operons or gene clusters as basic units,…

Performs homology searches with operons or gene clusters as basic units, instead of single genes. MultiGeneBlast allows users to get a better understanding of the function, evolutionary history, and…

Desktop app
BLAST DataBase Manager BLAST DataBase Manager

BDBM BLAST DataBase Manager

Provides a graphical user interface that allows to create high quality sequence…

Provides a graphical user interface that allows to create high quality sequence datasets using the tools included. BDBM permits to perform several common tasks such as doing BLAST alignments, getting…

Desktop app
BLAST Filter Tool BLAST Filter Tool

BFT BLAST Filter Tool

A Java software which implements a tool capable of filtering NCBI BLAST (Basic…

A Java software which implements a tool capable of filtering NCBI BLAST (Basic Local Alignment Search Tool) results with user-defined constraints. BFT contains the filtering engine to be used as a…

Desktop app
HitKeeper HitKeeper

HitKeeper

Controls the fully automatic handling of multiple biological databases and of…

Controls the fully automatic handling of multiple biological databases and of hit list calculations on a large scale. HitKeeper implements an asynchronous update system that introduces updates and…

Desktop app
Rapid Approach for… Rapid Approach for Seed optimization Based on a…
Desktop app
CTX-BLAST CTX-BLAST

CTX-BLAST

A software tool to incorporate contextual alignment model into the popular…

A software tool to incorporate contextual alignment model into the popular protein BLAST program. CTX-BLAST allows users to investigate the effect of context-dependency in the protein alignment much…

Desktop app
muBLASTP muBLASTP

muBLASTP

A database-indexed BLAST (Basic Local Alignment Search Tool) for protein…

A database-indexed BLAST (Basic Local Alignment Search Tool) for protein sequence search. muBLASTP delivers identical hits returned to NCBI BLAST. With its index structure for protein databases and…

Desktop app
G T A T C G C T A SequenceServer SequenceServer

SequenceServer

A modern graphical user interface for custom BLAST databases. SequenceServer…

A modern graphical user interface for custom BLAST databases. SequenceServer lets you rapidly set up a BLAST+ server with an intuitive user interface for use locally and for sharing with colleagues…

Desktop app
Nucleotide Similarity… Nucleotide Similarity Scanner

NSimScan Nucleotide Similarity Scanner

A tool for fast, sensitive and accurate DNA similarity search. Its targeted…

A tool for fast, sensitive and accurate DNA similarity search. Its targeted applications include phylogenomics, comparative and functional studies of non-coding sequences, contamination detection,…

Ascending Ladder… Ascending Ladder Program

ALP Ascending Ladder Program

Calculates the E-values for protein-protein or DNA-DNA local alignments of…

Calculates the E-values for protein-protein or DNA-DNA local alignments of random sequences, for arbitrary substitution score matrix, gap costs, and letter abundances. ALP allows insertion costs to…

Desktop app
High Speed BLASTN High Speed BLASTN

HS-BLASTN High Speed BLASTN

A parallel and fast nucleotide database search tool that accelerates…

A parallel and fast nucleotide database search tool that accelerates MegaBLAST—the default module of NCBI-BLASTN. HS-BLASTN builds a new lookup table using the FMD-index of the database and employs…

Desktop app
Parallel… Parallel Smith-Waterman Alignment Software

PaSWAS Parallel Smith-Waterman Alignment Software

Aligns DNA, RNA and protein sequences. It is possible (a) to have easy access…

Aligns DNA, RNA and protein sequences. It is possible (a) to have easy access to the computational power of NVIDIA-based general purpose graphics processing units (GPGPUs) to perform high-speed…

Desktop app
Smash tool Smash tool

Smash tool

A completely alignment-free method to find and visualise rearrangements between…

A completely alignment-free method to find and visualise rearrangements between pairs of DNA sequences. The detection is based on conditional exclusive compression, namely using a FCM, also known as…

Desktop app
Web app
Circoletto Circoletto

Circoletto

An online visualization tool based on Circos, which provides a fast,…

An online visualization tool based on Circos, which provides a fast, aesthetically pleasing and informative overview of sequence similarity search results.

Desktop app
KLAST KLAST

KLAST

A fast, accurate and NGS scalable bank-to-bank sequence similarity search tool…

A fast, accurate and NGS scalable bank-to-bank sequence similarity search tool providing significant accelerations (25x and more) of seeds-based heuristic comparison methods, such as the Blast suite…

Desktop app
PatternHunter PatternHunter

PatternHunter

A fast and sensitive general-purpose homology search tool, supporting DNA-DNA,…

A fast and sensitive general-purpose homology search tool, supporting DNA-DNA, Protein-Protein, translated DNA-protein, and translated DNA-DNA searches.

Desktop app
G-BLASTN G-BLASTN

G-BLASTN

A GPU-accelerated nucleotide alignment tool based on the widely used NCBI-BLAST.

A GPU-accelerated nucleotide alignment tool based on the widely used NCBI-BLAST.

Curators for Sequence homology search

  • Vincent Ranwez's avatar image
    Vincent Ranwez
    UMR AGAP, Montpellier…
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