Programs search nucleotide databases by using a nucleotide query. BLASTN key features are searching with short sequencing and cross-species comparison. Users can select an optimization according to: (i) highly similar sequences, (ii) more dissimilar sequences or (iii) somewhat similar sequences. This web application proceeds by searching sets in NCBI data sources.
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 strands) against a protein sequence database. This application can also work in Blast2Sequences mode and can send BLAST searches over the network to public NCBI server if desired.
Furnishes sequence similarity searching against protein databases. FASTA uses a protein query to offer a heuristic search. It can be combined with data retrieval to automate the coverage of the set of hit sequences found for a search. This tool allows researchers to specify their databank of interest, a protein, RNA or DNA sequence and to customize parameters through several functionalities.
A fully developed set of DNA sequence assembly (Gap4 and Gap5), editing and analysis tools (Spin). The package also covers most of the standard sequence analysis tasks such as restriction site searching, translation, pattern searching, comparison, gene finding, and secondary structure prediction, and provides powerful tools for DNA sequence determination.
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 TreeSeq that will run on Mac OS. This version of the software demonstrates the basic functionality.
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 differ from deletion costs. This has useful applications. For example, PacBio and nanopore DNA sequences have different insertion and deletion error rates, so accurate alignment should use different insertion and deletion costs. ALP also allows asymmetric score matrices, and different letter abundances in the two sequences.
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 small databases. It supports all 5 primary program types (blastn, blastp, tblastn, tblastx, and blastx) and several output formats (pairwise, tabular, or XML). ScalaBLAST will run on most multiprocessor systems that have Message Passing Interface (MPI) installed, and can run over a wide variety of interconnects including infiniband, quadrics, and ethernet.
Allows users to detect nucleotides sequences of interest. TBLASTX is a web application, part of the BLAST suite, intending to scan a or some sequence(s) to determine those which are similar according their coding potential. The platform supports multiple submission formats including bare sequences or identifiers and furnishes various optional features to exclude or limit the needed results as well as the possibility of targeting specific organisms.
Discovers short nucleotide or peptide sequences and patterns using Arabidopsis thaliana sequence datasets hosted in The Arabidopsis Information Resource (TAIR). PatMatch is a web application performing searches up to 20 residues and that supports both exact or approximate sequence matches. It also provides options allowing users to specify the number of hits that have to be returned or on which strand searching have to be run.
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 an accurate and effective seeding method to find short stretches of identities (called seeds) between the query and the database. HS-BLASTN produces the same alignment results as MegaBLAST and its computational speed is much faster than MegaBLAST.
Allows to spatially and temporally display influenza viruses related to a query sequence on a Google Map based on BLAST results against the NCBI Influenza Database. Temporal and geographical trends appear clearly and may help in reconstructing the evolutionary history of a particular sequence. MapMyFlu is accessible through a web server, hence without the need for local installation. The website has an intuitive design and provides an easy-to-use service.
Implements local alignment based on partition function posterior probabilities and is specifically tuned for aligning query ncRNA sequences to putative homologs in large genomes. PLAST-ncRNA is a server that replaces the portion of the target aligned to the query with a string of N’s of equal length and realigns the query. This server is designed specifically for BLAST like homology search and identifies all potential homologs in a target genome.
Recognizes sites of embedded ribonucleoside monophosphates (rNMPs). Ribose-Map permits users to investigate the nucleotide sequence context of these sites and explore their genome-wide distribution. It changes rNMP sequencing data created using any of the available rNMP sequencing techniques into summary datasets and publication-ready visualizations. This tool is useful for making head-to-head comparisons of studies.
Calculates covariance scores for constrained regions of background conservation. McBASC can be utilized as a covarying or highly conserved filter. This software gives an equally high score to conserved or covarying alignments and allows, without a reduction in score, substitution of conserved pairs of residues for covarying ones.
Aligns DNA, RNA and protein sequences. PaSWAS consists in a general-purpose graphics processing units (GPGPUs) implementation of the Smith-Waterman algorithm. The method is available through two different languages: Python and C, that give access to two different kinds of parallelization. The software allows the retrieval of information such as score, number of gaps and mismatches as well as the report of multiple hits per alignment.
Allows nucleotide and amino acid sequence similarity searches. ViroBLAST consists of a web-based interface to search against public sequence databases and local sequence databases, and an output interface to parse and navigate BLAST results. The software was developed for facilitating the verification of the origins of human immunodeficiency virus (HIV) sequences derived from various experiments. It is also available for download and installation and customization for any variety of specific projects.