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BLAST / Basic Local Alignment Search Tool
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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 matches to a query sequence. The software provides an access point for these tools to perform sequence alignment on the web. The set of BLAST command-line applications is organized in a way that groups together similar types of searches in one application.
ALP / Ascending Ladder Program
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 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.
GPU-BLAST / Graphics Processing Unit - Basic Local Alignment Search Tool
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 according to blastp algorithm (comparaison between protein sequences only). It uses the source code of the NCBI-BLAST but also GPU to accelerate execution. In comparison to the sequential NCBI-BLAST, the speedups achieved by GPU-BLAST range mostly between 3 and 4.
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 Tblastx). NOBLAST is an open source program that can be used with JAMBLAST, a graphic application that provides BLAST results management. It also offers an option to correct the statistics (E-value correction) when split databases are used (e.g. distributed BLAST in a grid or in a cluster) or when BLAST normalization is required (e.g. BLAST with a query set against several databases of different sizes).
NSimScan / Nucleotide Similarity Scanner
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, etc. NSimScan outperforms industry standard tools in combined sensitivity, accuracy and speed, operating at sensitivity similar to BLAST, accuracy of ssearch and speed of MegaBLAST. It has a particular advantage when searching for moderately distant similarities (60-90% identity) on massive datasets, making it useful for large-scale comparative analyses of DNA sequences.
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 maximum speed-up can be achieved on a given machine without negative effect on memory usage. It detects the maximum number of threads for the machine. The tool improves the user experience when working with large data. It is useful for NGS applications that involve annotation as an essential task.
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 practical applications of such genomic regions. It is fully equipped with applications to generate search databases from GenBank or from the user’s own sequence data. MultiGeneBlast provides a general search tool that can be exploited in a wide range of comparative genomics studies of homologous multigene units, by expert bioinformaticians and experimental biologists alike.
rasbhari / Rapid Approach for Seed optimization Based on a Hill-climbing Algorithm that is Repeated Iteratively
Calculates sets of binary patterns for read mapping, database searching and alignment-free sequence comparison. For sequence-homology searching, Rasbhari optimizes the sensitivity of pattern sets. Since the sensitivity of a pattern set is expensive to calculate, the algorithm optimizes the overlap complexity of the produced pattern sets which is closely related to its sensitivity.
JCoast / Java Comparative Analysis and Search Tool
Analyzes individual and cross genome- and metagenome sequences by taking into account multiple projects simultaneously. JCoast is a standalone application, based on GenDB, available on both API and GUI. On a part, the GUI allows users to handle genomic information with functionalities such as dedicated modules for addressing or comparative statistics based on profile-Hidden Markov models. On other part, the API permits to generate object relational mapping and specific classes for advanced searches, data mining and statistics.
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 associated optimizations, muBLASTP is a re-factored BLASTP algorithm for modern multicore processors that achieves much higher throughput with acceptable memory usage for the database index. Those optimizations and techniques in index structure and BLAST algorithm, such as index compression, sorting index, two level binning, etc., are not merely beneficial to database-indexed search for protein sequence, also can be propagated to nucleotide sequence search and other alignment algorithms.
SparkBLAST / Spark Basic Local Alignment Search Tool
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 uses Apache Spark as the coordination framework. It was evaluated on both Google and Microsoft Azure Clouds, for several configurations and dataset sizes. The tool is able to achieve, in average, a maximum speedup of 41.78, reducing the execution time from 28,983 s in a single node, to 693 s in 64 nodes.
Quantifies genomic relationships on the basis of gene connection model. Newdist provides implementations of three similarity measures of different expression power. It includes an intermediate approach between family-based and family-free genomic similarity measures, gene connections. It requires some preprocessing of the genes contained in the genomes under study. It facilitates the inter-species comparison of gene orders between two genomes by means of counting conserved adjacencies.
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 over the web. SequenceServer has been used for research on emerging model organisms (e.g., sea cucumber, starfish, falcons, Hessian fly, sugar-apple tree, Streptocarpus rexii), and for research in bioadhesion and environmental microbiology. SequenceServer is a main querying mechanism for several community databases (e.g., Drosophila suzukii, planarians, birch and ash tree, Amborella, echinoderms, Fusarium, ants, butterfly), and is also used as an educational resource.
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 computes hits as soon as new data become available. It provides a generic and modular framework to handle the redundancy and incremental updates of biological databases, and an original query language. The query syntax enables the user to specify constraints for searching proteins, such as retrieving sequences that contain specific motifs, or a defined arrangement of motifs, or queries based on the classification of sequences.
BEAP / BLAST Extension and Alignment Program
Allows sequence searching and assembling. BEAP is able to identify orthologous genes for positional cloning. It can find gene sequences in contigs by returning contigs spanning exons and flanking intronic sequences. This tool can recognize sequence mismatch that may represent possible single nucleotide polymorphisms (SNPs). It allows users to specify local or remote database querying, stringency of BLAST hits, and word size within the megaBLAST option.
SRD / Sequence Relation Drawing program
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 consists of two components: a Window-based application and a computerized database. It helps to investigate traits of the spread of the AIDS disease, which may help biologists or clinicians to control the AIDS disease transmission in molecular epidemiology study.
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