Search Results for "blast"
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Showing 113 open source projects for "blast"
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Ship Agents FasterGemini Enterprise Agent Platform lets you rapidly build, scale, govern and optimize production-ready agents grounded in your organization's data. The platform enables developers to build custom or pre-built agents for virtually any use case. New customers get $300 in free credits.
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MongoDB Atlas runs apps anywhereMongoDB Atlas gives you the freedom to build and run modern applications anywhere—across AWS, Azure, and Google Cloud. With global availability in over 115 regions, Atlas lets you deploy close to your users, meet compliance needs, and scale with confidence across any geography.
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Evolver
The GEP-Powered Self-Evolution Engine for AI Agents
...The project uses a protocol-constrained approach centered on concepts such as genes, capsules, and events, which are stored as structured assets and selected through signal matching logic. It also depends on Git as part of its operating model, using repository state for rollback, blast-radius calculation, and solidification workflows, which makes it especially relevant for code-centric agent environments. The CLI integrates with external agent runtimes through setup hooks, including support for platforms such as Cursor, where hooks can fire at specific lifecycle moments like session start or after file edits. -
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BRIG is a cross-platform (Windows/Mac/Unix) application that can display circular comparisons between a large number of genomes, with a focus on handling genome assembly data. Please cite the BRIG paper if BRIG is used to generate figures for publications: NF Alikhan, NK Petty, NL Ben Zakour, SA Beatson (2011) BLAST Ring Image Generator (BRIG): simple prokaryote genome comparisons, BMC Genomics, 12:402. PMID: 21824423
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MDX
Markdown for the component era
MDX lets you use JSX in your markdown content. You can import components, such as interactive charts or alerts, and embed them within your content. This makes writing long-form content with components a blast. -
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Chaos Mesh
A Chaos Engineering Platform for Kubernetes
...Chaos Mesh provides multiple filtering rules that allow selecting injection targets based on labels, annotations, and so on. They are collectively called selectors. In addition, users can also set a namespace whitelist to greater control the "blast radius" of the experiment. -
Stop vibe-debugging.AppSignal's MCP server hands Claude, Cursor, or Zed your real errors, traces, and the deploy that shipped them. AI writes the fix; you review the diff.
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MView
Extract and reformat a sequence database search or multiple alignment
.... ---- MView is a command line utility that extracts and reformats the results of a sequence database search or a multiple alignment, optionally adding HTML markup for web page layout. It can also be used as a filter to extract and convert searches or alignments to common formats. Inputs: - Sequence database search: BLAST, FASTA suites. - Multiple sequence alignment: CLUSTAL, HSSP, MSF, FASTA, PIR, MAF. Outputs: - HTML, FASTA, CLUSTAL, MSF, PIR, RDB (tab-separated). Found a bug? Please open an issue on the MView issue tracker at https://github.com/desmid/mview/issues or send an email to biomview@gmail.com. -
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FindPlasmids
Find plasmids in microbial genome assembly files
FindPlasmids identifies known plasmids in genome assembly files by using the assembly file to query a local Blast+ database of plasmid sequences. The FindPlasmids package includes executables for Mac OS X, Linux and Windows. Detailed instructions for making the local plasmid database, searching it, and identifying the plasmids are included in the FindPlasmids package. -
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Seqs Extractor is a useful tool, and can reduce ambiguities in analyses which uses BLAST command ine, commonly in the next generation sequencing, Transcriptomics, Proteomics, etc and help extract BLASTed sequences and sequences that contains microsatellites. Seqs Extrator also turns the BLAST command line more friendly.
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BADASS is a software with a user-friendly graphical interface applied to the search and analysis of bacteriocin diversity in whole-metagenome shotgun sequencing data. The search for bacteriocin sequences is performed with tools such as BLAST or DIAMOND using the BAGEL4 database as a reference. The putative bacteriocin sequences identified are used to determine the abundance and richness of the three classes described so far. Abundance is calculated by comparing the reads identified as bacteriocins to the reads identified as 16S rRNA gene using SILVA database as a reference. ...
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A fungal genome annotation pipeline (funnote) integrated by CAIQ (Chinese Academy of Inspection and Quarantine). ## prerequisites 1. skewer (https://github.com/relipmoc/skewer) 2. BLAST (https://blast.ncbi.nlm.nih.gov/) 3. DIAMOND (https://github.com/bbuchfink/diamond) 4. funannotate (https://github.com/nextgenusfs/funannotate) 5. InterProScan (https://github.com/ebi-pf-team/interproscan) 6. emapper (https://github.com/eggnogdb/eggnog-mapper)
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Fully Managed MySQL, PostgreSQL, and SQL ServerCloud SQL handles your database ops end to end, so you can focus on your app.
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Cylindrical Alignment App
Arranges alignments in a rotating cylinder
The Cylindrical Alignment App is the successor to Cylindrical BLAST Viewer. Similarly, it arranges search or other comparisons, against their "axis". Searches can be made by Basic Local Alignment Search Tool, ClustalW, or Gene Machine to name a few. This version does not require downloading or installing Java3D, and has more modern GUI features. -
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KimBlast
Blast+ the easy way
KimBlast GUI formats and indexes Fasta databases for Blast, performs Blast searches and analyzes results. Python 3.x version. For more information, you can have a look at the README.md file in the source code tree: https://sourceforge.net/p/lp-csic-uab/kimblast3/code/ci/default/tree/README.md -
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ASGARD
Metabolic reconstruction from DNA or protein sequences.
ASGARD is software for metabolic pathway reconstruction, but it can also generate other types of biological sequence annotation (EC and GO numbers, BLAST reports). This program is intended to be run in UNIX-like systems, and supports SGE or PBS. -
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GenSeed-HMM
Progressive assembly tool using DNA, protein or profile HMMs as seeds.
...Basically, GenSeed-HMM performs three operations, repeatedly: - recruit reads by matching them to a seed - assemble the recruited reads (including previously assembled contigs) - generate new seeds (for the next round of progressive assembly) from the extremities of all generated contigs The first seed is provided by the user, and can be a piece of DNA or protein sequence, or an HMM profile, for increased sensitivity. This program depends on BLAST+ or hmmsearch and a number of third-party support tools (EMBOSS' transeq and splitter, bowtie, 454's sfffile and sffinfo). Which tools will be mandatory depends on the kind of seed and assembler used. Assemblers currently supported include CAP3, Newbler, SOAPdenovo, Velvet, and Abyss. -
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VR Radio Helper
VR-Optimized ATC/Radio Plugin for X-Plane + FlyWithLua
...It allows changing the two main COM frequencies of any X-Plane airplane in Virtual Reality via convenient touch pad number buttons in a multi-crew environment. For many default airplanes, NAV, Transponder and Barometer can be changed as well. Flying VR multi-crew in X-Plane with ATC is a blast! Yet, the default X-Plane 11 VR knobs are horrible when trying to monitor/fly and dial in a new ATC frequency at the same time (takes up to 2 minutes for a 2-hour flight, just turning the knob and making sure that no turn got lost when using SmartCopilot). It replaces most ATC/navigation-related knobs with a number panel, like COM, NAV, Transponder and Barometer settings. ... -
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parallelblast_plus
Database sliced Blast implementation
Updated versions of programs described in: Parallel BLAST on split databases" Bioinformatics 2003 Sep 22;19(14):1865-6. https://doi.org/10.1093/bioinformatics/btg250 but which now work with modern BLAST versions. -
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TaxOnTree
A program for associating taxonomic information in a phylogenetic tree
...The output is a NEX format tree file configured to be opened in FigTree, that users can promptly color by any taxa or by the ancestrality shared by sequences with query. Input can be a Fasta formatted file to be used in a BLAST search or a list of sequences represented by their identifiers (UniProtAC or NCBI gi), if a cluster is already available. Also, a newick file produced with user software and specific settings can be used to proceed with the taxonomic labeling. TaxOnTree turns its user into an expert on taxonomy. TaxOnTree also corrects for the absence of some taxa in NCBI taxonomy. ... -
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seqdiva
SeqDivA:Sequence Diversity Analysis
Sequence Diversity Analysis - SeqDivA version 1.0 is a python-based tool with a friendly GUI designed for Linux and Mac OS. Utility: Run alignment algorithms (water, needle, and blast) to compare all-vs.-all protein, DNA, and RNA sequences. SeqDivA provides similarity, identity, and bit-score matrixes and dot plots to explore/illustrate the diversity (homology degree) of the sequences, enabling the delimitation of the twilight zone. Installation: - Download SeqDivA - decompress the “.zip or tar.gz” file - Load the graphical interface by executing python SeqDivA.py. ... -
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MetaErg
Metagenome Annotation Pipeline
MetaErg is a stand-alone and fully automated metagenome and metaproteome annotation pipeline published at: https://www.frontiersin.org/articles/10.3389/fgene.2019.00999/full. If you are using this pipeline for your work, please cite: Dong X and Strous M (2019) An Integrated Pipeline for Annotation and Visualization of Metagenomic Contigs. Front. Genet. 10:999. doi: 10.3389/fgene.2019.00999 The instructions on configuring and running the MetaErg pipeline is available at GitHub... -
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Node.js chaos monkey
Extremly naughty chaos monkey for Node.js
...It lets teams rehearse real-world incidents—latency spikes, random process exits, resource exhaustion—and observe how circuits, retries, and backoff strategies behave. The tool is designed to be safe and configurable, enabling narrow blast radii and scheduled experiments during non-critical windows. It integrates naturally with staging or even carefully guarded production environments where you want confidence instead of assumptions. Findings feed back into reliability work: hardening timeouts, rethinking concurrency limits, and improving fallbacks at code and infrastructure levels. ... -
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Light Bright in Python
The classic toy reinvented in free software!
...I was given the honor to demonstrate software engineering at an event to help introduce young women to the various fields of engineering. This project was made just for the occasion! I had a blast making it and I hope everyone enjoys this FOSS just as much. The simple design and well-commented code is a great example of turning an everyday object into a shareable program for others to enjoy. Requires Python 3.7 and Pygame 1.9.6. These are FREE: Python Download: https://www.python.org/downloads/ Python/Pygame install YouTube tutorial: https://www.youtube.com/watch?... -
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Neat
A lightweight and flexible Sass grid
Neat is a fluid grid framework with the aim of being easy enough to use out of the box and flexible enough to customize down the road. Neat also works great with Bourbon and Bitters, They are all lightweight and easy to work with so it’s a blast to try them out and see if they’re right for your next project. If you need multiple grids in a single project, you can do this by defining a new map stored within a variable of your choosing. This variable can then be passed directly into any of Neat's mixins. Custom grids are especially useful with grid-media. By defining a media attribute within your custom grid, you are able to easily define gutter width and total column count as well as the breakpoint at which they should activate. ... -
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FHiTINGS
Fungal High-throughput Taxonomic Identification tool for use with NGS
...See our paper in the Journal of Basic Microbiology (http://onlinelibrary.wiley.com/doi/10.1002/jobm.201200507/pdf) for more information and please cite that paper if you use our program. Thank you for using FHiTINGS! Note: FHiTINGS version 1-4 has been released. This uses an update to the BLAST database used by FHiTINGS. Also note that FHiTINGS must run on Python 2.4-2.7.1 (it will NOT run on Python 3.0 or higher). © 2012 by Karen Dannemiller. FHiTINGS is made available under the terms of the Creative Commons Attribution-ShareAlike 3.0 license, http://creativecommons.org/licenses/by-sa/3.0/. Other related projects: Aspergillus databases for FHiTINGS, http://sourceforge.net/projects/aspdbforfhitings/ -
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ALDB
ALDB: a domestic-animal long noncoding RNA database
...Moreover, ALDB provides related useful data, such as genome-wide expression profile and animal quantitative trait loci (QTLs), that is not available in the existing lncRNA database (lncRNAdb and NONCODE), along with convenient tools, such as BLAST, GBrowse and flexible search functionalities. Aimin Li, PhD School of Computer Science and Engineering, Xi'an University of Technology, 5 South Jinhua Road, Xi'an, Shaanxi 710048, P.R China liaiminmail AT gmail.com emanlee815 AT 163.com -
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LBXR - LOAD BLAST XML RESULTS O sistema permite que sejam importados resultados obtidos por meio de pesquisas de similaridade a partir do BLAST, com resultados gerado no formato XML para o banco de dados relacional MariaDB ou MySQL.
