Search Results for "blast"
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Showing 112 open source projects for "blast"
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Chaos Mesh
A Chaos Engineering Platform for Kubernetes
... 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. -
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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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MView
Extract and reformat a sequence database search or multiple alignment
...: - 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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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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NeoLoad is a very comprehensive tool if you are looking for a performance test tool for web applications and other applicationsYour applications are all built differently, but they all need to perform. NeoLoad simplifies and scales performance testing for everything, from APIs and microservices, to end-to-end application testing through innovative protocol and browser-based capabilities.
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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...
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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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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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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 -
Multi-Site Network and Cloud Connectivity for BusinessesAs your users rely more and more on Cloud and Internet-based technologies, reliable internet connectivity becomes more and more important to your business. With Bigleaf’s proven SD-WAN architecture, groundbreaking AI, and DDoS attack mitigation, you can finally deliver the reliable internet connectivity your business needs without the limitations of traditional networking platforms. Bigleaf’s Cloud Access Network and plug-and-play router allow for limitless control to and from anywhere your traffic needs to go. Bigleaf’s self-driving AI automatically identifies and adapts to any changing circuit conditions and traffic needs—addressing issues before they impact your users. Bigleaf puts you in the driver’s seat of every complaint and support call with full-path traffic and network performance data, delivered as actionable insights, reports, and alerts.
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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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VR Radio Helper
VR-Optimized ATC/Radio Plugin for X-Plane + FlyWithLua
VR Radio Helper is a FlyWithLua plugin for X-Plane 11. 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... -
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GenSeed-HMM
Progressive assembly tool using DNA, protein or profile HMMs as seeds.
... 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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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
TaxOnTree is a phylogenetic 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... -
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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... -
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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... -
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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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Light Bright in Python
The classic toy reinvented in free software!
... 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?v=AdUZArA-kZw -
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FHiTINGS
Fungal High-throughput Taxonomic Identification tool for use with NGS
... 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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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.
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ALDB
ALDB: a domestic-animal long noncoding RNA database
...), 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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pydictor
powerful and useful hacker dictionary builder for a brute-force attack
A powerful and useful hacker dictionary builder for a brute-force attack. You can use pydictor to generate a general blast wordlist, a custom wordlist based on Web content, a social engineering wordlist, and so on; You can use the pydictor built-in tool to safe delete, merge, unique, merge and unique, count word frequency to filter the wordlist, besides, you also can specify your wordlist and use '-tool handler' to filter your wordlist. You can generate highly customized and complex wordlists... -
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idwtree
Assigns orthologs using a phylogenetic tree
Protein BLAST analysis finds all homologs of a protein; however, for many analyses, it is important to identify orthologs in different species (e.g. homologs that derive from the same ancestral sequence). The program idwtree aid in this analysis by assigning 'group' identity in phylogenetic trees containing reference sequences as markers. The standard workflow idwtree was intended to analyze: 1. BLAST protein sequence of interest against organism(s) of interest. 2... -
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A comparative synteny analysis tool for target-gene SNP marker discovery: connecting genomics data to breeding in Solanaceae * The foundation of this web source is CodeIgniter. * After setting the CodeIgniter framework, unzip it under the default home directory. The database is based on Maria DB (mysql). Download the schema and import it into the DB. Each species you want to analyze needs blast results. Fit the fields to match the schema and it will work.