Main logo
?
tutorial arrow
×
Submit new tools
Share tools covering the current topic. Provide easy-to-follow guidelines to improve their usability.
Share new tools with the community
Sign up for free to promote the availability of bioinformatics tools

Protein database search software tools | Shotgun metagenomic sequencing data analysis

In metagenomics studies, millions of DNA or cDNA reads are sequenced from environmental samples, and these are then analyzed in an attempt to determine the functional or taxonomic content of the samples (Handelsman et al., 1998). An important…
G T A T C G C T A
SUPER-FOCUS
Desktop

SUPER-FOCUS SUbsystems Profile by databasE Reduction using FOCUS

An agile homology-based approach using a reduced reference database to report…

An agile homology-based approach using a reduced reference database to report the subsystems present in metagenomic datasets and profile their abundances. SUPER-FOCUS was tested with over 70 real…

G T A T C G C T A
BLASTX
Web

BLASTX Translated BLAST: blastx

Searches protein database using a translated nucleotide query. BLASTX is a…

Searches protein database using a translated nucleotide query. BLASTX is a BLAST search application that compares the six-frame conceptual translation products of a nucleotide query sequence (both…

G T A T C G C T A
BLAT
Desktop
Web

BLAT BLAST-Like Alignment Tool

Finds genomic sequences that match a protein or DNA sequence submitted by the…

Finds genomic sequences that match a protein or DNA sequence submitted by the user. BLAT is a very fast sequence alignment tool similar to BLAST typically used for searching similar sequences within…

G T A T C G C T A
DIAMOND
Desktop

DIAMOND

An alignment tool for aligning short DNA sequencing reads to a protein…

An alignment tool for aligning short DNA sequencing reads to a protein reference database such as NCBI nonredundant (NCBI-nr). On Illumina reads of length 100-150bp, in fast mode, DIAMOND is about…

G T A T C G C T A
Taxonomer
Web

Taxonomer

An ultrafast web-tool for comprehensive metagenomics data analysis and…

An ultrafast web-tool for comprehensive metagenomics data analysis and interactive results visualization. Taxonomer is unique in providing integrated nucleotide and protein-based classification and…

G T A T C G C T A
Consensus…
Desktop

Consensus Sequence Searches

Allows users to search and align databases of consensus sequences. ConSequenceS…

Allows users to search and align databases of consensus sequences. ConSequenceS is a method for consensus sequence-based comparisons that improves searches and alignments as an add-on to PSI-BLAST.

G T A T C G C T A
H-BLAST
Desktop

H-BLAST Heterogeneous BLAST

Provides a fast parallel search tool for a heterogeneous computer that couples…

Provides a fast parallel search tool for a heterogeneous computer that couples CPUs (Central Processing Units) and GPUs (Graphics Processing Units), to accelerate BLASTX and BLASTP - basic modules of…

G T A T C G C T A
MMseqs
Desktop

MMseqs Many-against-Many sequence searching

Allows clustering and searching of large protein datasets, such as UniProt, or…

Allows clustering and searching of large protein datasets, such as UniProt, or 6-frame translated metagenomics sequencing reads. MMseqs is a software suite which contains three core modules: a…

G T A T C G C T A
SANSparallel
Web

SANSparallel

Provides protein sequence database searches with immediate response and…

Provides protein sequence database searches with immediate response and professional alignment visualization by third-party software. The database search uses the suffix array neighborhood search…

G T A T C G C T A
PALADIN
Desktop

PALADIN Protein ALignment And Detection INterface

A modification of Burrows-Wheeler Aligner that provides more accurate alignment…

A modification of Burrows-Wheeler Aligner that provides more accurate alignment and orders-of-magnitude improved efficiency by directly mapping in protein space. In brief, PALADIN identifies and…

G T A T C G C T A
SWORD
Desktop

SWORD Smith Waterman On Reduced Database

Combines a heuristic and an exact approach. It is aimed to replace BLAST, as it…

Combines a heuristic and an exact approach. It is aimed to replace BLAST, as it is faster between 8 and 16 times and has better or comparable sensitivity. The second main advantage is that it…

G T A T C G C T A
FALP
Desktop

FALP Frameshift Ascending Ladder Program

Calculates the statistical parameters in the modified Gumbel distribution for…

Calculates the statistical parameters in the modified Gumbel distribution for gapped alignment with frameshifts. FALP allows arbitrary genetic codes, and does not assume that translated DNA has…

G T A T C G C T A
PSI-BLAST
Web
Desktop

PSI-BLAST Position-Specific Iterated Basic Local Alignment Search Tool

Allows to find regions of sequence similarity. PSI-BLAST is a protein database…

Allows to find regions of sequence similarity. PSI-BLAST is a protein database search program. The software is able to access the probable substitutions at each sequence position using the results of…

G T A T C G C T A
AlignBucket
Desktop

AlignBucket

A software tool for splitting a fasta file into smaller pieces suitable for…

A software tool for splitting a fasta file into smaller pieces suitable for alignment with BLAST. AlignBucket optimizes the partition of a large volume of sequences (the whole database) into sets…

G T A T C G C T A
MetaQuery
Desktop
Web

MetaQuery

A web application for rapid and quantitative analysis of specific genes in the…

A web application for rapid and quantitative analysis of specific genes in the human gut microbiome. MetaQuery takes as input a multi-FASTA file containing one or more protein sequences, and returns…

G T A T C G C T A
GHOSTZ
Desktop

GHOSTZ

A fast homology search method based on database subsequence clustering. GHOSTZ…

A fast homology search method based on database subsequence clustering. GHOSTZ clusters similar subsequences from a database to perform an efficient seed search and ungapped extension by reducing…

G T A T C G C T A
GHOSTM
Desktop

GHOSTM GPU-based HOmology Search Tool for Metagenomics

A homology search tool for huge short reads generated by next-generation…

A homology search tool for huge short reads generated by next-generation sequencers. The system first searches for candidate alignment positions for a sequence from the database using pre-calculated…

G T A T C G C T A
SW#db
Desktop

SW#db

A parallelised version of exact database search algorithms optimised for…

A parallelised version of exact database search algorithms optimised for multiple queries. Although the emphasis is on the Smith-Waterman algorithm, other exact algorithms such as global and…

G T A T C G C T A
Qudaich
Desktop

Qudaich Queries and unique database alignment inferred by clustering homologs

A sequence aligner which can efficiently process large volumes of data and is…

A sequence aligner which can efficiently process large volumes of data and is suited to de novo comparisons of next generation reads datasets. Qudaich performs local sequence alignments in two major…

G T A T C G C T A
Lambda
Desktop

Lambda

A BLAST compatible local aligner optimized for NGS and protein searches. It is…

A BLAST compatible local aligner optimized for NGS and protein searches. It is faster than most other tools around while maintaining a high sensitivity. In contrast to some of the other programs,…

G T A T C G C T A
PAUDA
Desktop

PAUDA Protein Alignment Using a DNA Aligner

An approach toward the problem of comparing DNA reads against a database of…

An approach toward the problem of comparing DNA reads against a database of protein reference sequences that is applicable to very large datasets consisting of hundreds of millions or billions of…

G T A T C G C T A
RAPSearch
Desktop

RAPSearch Reduced Alphabet based Protein similarity Search

A fast protein similarity search tool that utilizes a reduced amino acid…

A fast protein similarity search tool that utilizes a reduced amino acid alphabet and suffix array to detect seeds of flexible length. RAPSearch2 works faster than the original RAPSearch; uses less…

G T A T C G C T A
GHOSTX
Desktop

GHOSTX

A homology search tool which can detect remote homologues like BLAST and is…

A homology search tool which can detect remote homologues like BLAST and is about 100 times more efficient than BLAST by using suffix arrays. GHOSTX achieved approximately 131–165 times…

G T A T C G C T A
MICA
Desktop

MICA Metagenomic Inquiry Compressive Acceleration

A framework for similarity search based on characterizing a data set’s…

A framework for similarity search based on characterizing a data set’s entropy and fractal dimension. MICA is an accelerated version of standard tools with no loss in specificity and little loss in…

G T A T C G C T A
Tachyon
Web

Tachyon

Quickly connects a query protein sequence to highly similar sequences and…

Quickly connects a query protein sequence to highly similar sequences and selected associated resources. Tachyon identifies closely related protein sequences ~200 times faster than standard BLAST,…

Information

By using OMICtools you acknowledge that you have read and accepted the terms of the end user license agreement.