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Nucleotide sequence homology search software tools | Comparative genomics

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) High speed BLASTN: an accelerated MegaBLAST search tool. Nucleic…
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…

TreeSeq
Desktop

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…

TBLASTX
Web

TBLASTX Translated BLAST: tblastx

Search translated nucleotide database using a translated nucleotide query.

Search translated nucleotide database using a translated nucleotide query.

BLASTN
Web

BLASTN Standard Nucleotide BLAST

Programs search nucleotide databases using a nucleotide query. BLASTN key…

Programs search nucleotide databases using a nucleotide query. BLASTN key features are searching with short sequencing and cross-species comparison.

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.

TBLASTN
Web

TBLASTN Translated BLAST

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…

WU-BLAST
Web

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.

FASTA
Web

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.

ENA Sequence…
Web

ENA Sequence Search

Allows users to search sequence similarity.

Allows users to search sequence similarity.

GPU-BLAST
Desktop

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…

MultiGeneBlast
Desktop

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…

PatMaN
Desktop

PatMaN

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

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

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…

G-BLASTN
Desktop

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.

ALP
Desktop

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…

Oracle…
Desktop

Oracle Database 10g

Offers a range of improved data management and data sharing features that can…

Offers a range of improved data management and data sharing features that can support the biology domain. Oracle Database 10g provides a distributed data architecture. It allows users to write…

Alfy
Desktop

Alfy ALignment-Free local homologY

Allows users to identify closest homologs. Alfy performs this identification in…

Allows users to identify closest homologs. Alfy performs this identification in three steps: (1) it begins by constructing an enhanced suffix array of query and subject sequences; (2) the array is…

HS-BLASTN
Desktop

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…

kWIP
Desktop

kWIP k-mer Weighted Inner Product

Estimates genetic similarity by using an assembly- and alignment-free method.…

Estimates genetic similarity by using an assembly- and alignment-free method. kWIP combines a probabilistic data structure with the weighted inner product (WIP) to calculate pairwise similarity…

Bridges
Desktop

Bridges

Identifies local similarities between sequences by using short exact word…

Identifies local similarities between sequences by using short exact word matches. Bridges can perform multiple queries that are individually compared to the database. Besides, users can compare…

ScalaBlast
Desktop

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…

NSimScan
Desktop

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,…

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…

Zerg
Desktop

Zerg

Provides users a parser library that could be used by a wide variety of…

Provides users a parser library that could be used by a wide variety of programs. Zerg is a C library for parsing the output of NCBI BLAST programs. The library design is simple in sense that its…

JAMBLAST
Desktop

JAMBLAST Java Application Manager for ncbi BLAST

Allows the user to manage BLAST files. JAMBLAST is a graphic application that…

Allows the user to manage BLAST files. JAMBLAST is a graphic application that provides BLAST results produced with the NOBLAST, a user-friendly tabular output format for various NCBI BLAST programs…

rasbhari
Desktop
SWIPE
Desktop
CrocoBLAST
Desktop

CrocoBLAST

Facilitates the application of BLAST+ in the analysis of Next Generation…

Facilitates the application of BLAST+ in the analysis of Next Generation Sequencing (NGS) data. CrocoBLAST runs a pre-calculation to estimate the optimal size of the temporary input files so that…

CTX-BLAST
Desktop

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…

muBLASTP
Desktop

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…

PaSWAS
Desktop

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…

USM
Web

USM Universal Sequence Map

Allows users to treat sequence comparison that can be decomposed in several…

Allows users to treat sequence comparison that can be decomposed in several rounds of map and reduce operations. USM performs decomposition and parallelization of sequence alignment to anticipate a…

NOBLAST
Desktop

NOBLAST

Provides an extended user friendly csv output format and offers an option to…

Provides an extended user friendly csv output format and offers an option to correct the statistics when split databases are used for NCBI BLAST programs (Blastn, Blastp, Blastx, Tblastn and…

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…

BlastXtract
Desktop

BlastXtract

Facilitates early exploration of un-annotated genomic and metagenomic…

Facilitates early exploration of un-annotated genomic and metagenomic sequences. BlastXtract focuses and uses translated searches from a wider range of commonly used tools. It permits to make rapid…

BDBM
Desktop

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…

BFT
Desktop

BFT BLAST Filter Tool

Implements a tool capable of filtering NCBI BLAST (Basic Local Alignment Search…

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 command-line tool and a…

G T A T C G C T A
SequenceServer
Desktop

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…

Smash tool
Desktop

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…

Circoletto
Desktop
Web

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.

CLAST
Desktop

CLAST CUDA implemented large-scale alignment search tool

Identifies weak sequence similarity with both short and long query read…

Identifies weak sequence similarity with both short and long query read lengths. CLAST intends to detect similar regions between query and reference genome sequences and products taxonomic…

STELLAR
Desktop

STELLAR SwifT Exact LocaL AligneR

Brings exact local alignments to the community at the speed of heuristic…

Brings exact local alignments to the community at the speed of heuristic state-of-the-art tools like BLAST, BLAT, or LASTZ. STELLAR is an algorithm to compute all local alignments of a minimal length…

MyDbFinder
Web

MyDbFinder MyDatabaseFinder

Provides multipurpose detection of genetic markers. MyDbFinder is a web…

Provides multipurpose detection of genetic markers. MyDbFinder is a web application that identifies genes from users’ database in total or partial sequenced isolates of bacteria. It must be in…

seg-suite
Desktop

seg-suite

Contains a toolkit for arranging segments, alignments, and annotations of…

Contains a toolkit for arranging segments, alignments, and annotations of sequences. seg-suite performs composing alignments and is composed of a conversion program which transforms various formats…

SSW
Web
Desktop

SSW Striped Smith-Waterman

Provides users a library for use in genomic applications. SSW is a fast…

Provides users a library for use in genomic applications. SSW is a fast implementation of the Smith-Waterman algorithm, which uses the Single-Instruction Multiple-Data (SIMD) instructions to…

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…

Renkan Blast
Web

Renkan Blast

Blasts query sequences on 18S and 28S radiolaria databases. Renkan Blast…

Blasts query sequences on 18S and 28S radiolaria databases. Renkan Blast permits to search a nucleotide database using a nucleotide query, using the NCBI BLAST and blastn command line tool.…

Cyanorak Blast
Web

Cyanorak Blast

Blasts query sequences on Synechococcus and Prochlorococcus strains. Cyanorak…

Blasts query sequences on Synechococcus and Prochlorococcus strains. Cyanorak Blast is a web application that permits to search (i) nucleotide database with nucleotide query sequences, (ii) protein…

dbiblast
Desktop

dbiblast

Indexes a blast database created by the NCBI indexing programs formatdb,…

Indexes a blast database created by the NCBI indexing programs formatdb, pressdb or setdb, and builds EMBL CD-ROM format index files. This format is used by dbiblast on the EMBL database CD-ROM…

HitKeeper
Desktop

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…

KLAST
Desktop

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…

PatternHunter
Desktop

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.

MplusD
Desktop

MplusD

Proposes statistical measures to compare biological sequences to further their…

Proposes statistical measures to compare biological sequences to further their alignments, structures, functions and evolutionary information. MplusD is able to perfom similarity search and evaluate…

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…

PARIGA
Web

PARIGA

Enables users to perform all-against-all BLAST searches on two sets of…

Enables users to perform all-against-all BLAST searches on two sets of sequences selected by the user. PARIGA allows the user to filter outputs by using several parameters in real-time fashion,…

SmartBlast
Web

SmartBlast

Processes protein query to present a concise summary of the five best protein…

Processes protein query to present a concise summary of the five best protein matches from well-studied reference species in the landmark database. SmartBLAST uses a combination of BLAST searches and…

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