Search Results for "bacteria"
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Showing 28 open source projects for "bacteria"
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Prokka
Rapid prokaryotic genome annotation
Prokka is a command-line software tool for rapid annotation of prokaryotic genomes (bacteria and archaea). Given a FASTA file of contigs, it predicts genes, rRNAs, tRNAs, and other functional elements, then assigns functions by comparing to reference protein databases and HMM profiles. It outputs GenBank, GFF, and other formats compatible with downstream tools and genome browsers. Prokka handles common complications—overlapping ORFs, frameshifts, alternate start codons—while providing customizable databases so researchers can bias domain or strain-specific annotations. ... -
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Gemi
PCR primers / probes design from multiple & degenerate sequences
Gemi, an automated, fast, and easy-to-use bioinformatics tool with a user-friendly interface to design primers and probes for polymerase chain reaction (PCR). Gemi accepts multiple aligned and long DNA and RNA sequences with degenerate nucleotide (non-A/C/G/T bases). Gemi can be used for quantitative, real-time and conventional PCR (qPCR, rt-PCR, etc.), and Sanger sequencing. Gemi can parse large dataset of sequences efficiently. Python source code is available upon request. Milestone:... -
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PANDORA
Revolutionizing Biomedical Research with Advanced Machine Learning
PANDORA is a machine learning (ML) tool that can be used to integrate various data types, including clinical, transcriptome and microbiome data and find connections in large datasets. PANDORA can be easily installed using Docker, a pre-built version of the software can be pulled from DockerHub. In order to run a test instance of PANDORA, users will first need to prepare their local environment by downloading, installing, and configuring Docker. genular is a community behind SIMON an... -
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rafah
Random Forest Assignment of Hosts
One fundamental question when trying to describe viruses of Bacteria and Archaea is: Which host do they infect? To tackle this issue we developed a machine-learning approach named Random Forest Assignment of Hosts (RaFAH), which outperformed other methods for virus-host prediction. Our rationale was that the machine could learn the associations between genes and hosts much more efficiently than a human, while also using the information contained in the hypothetical proteins. -
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metatea
METATEA enables fast 16S rRNA-based analyses at the sequence level
...However, you should use the same primers and sequencing platform for the sequence-supervised approaches. ○ Exclusive correlation value (ECV) was defined for the detection of mutually exclusive relationships between bacteria like probiotics and pathogens that are antagonistic each other. You can draw ECV network using ECV matrix from METATEA. ○ METATEA is originally desigend and developed by a talented Post. Doc Seunguk Shin in Yonsei University. If many persons use METATEA and request new functions, more functions will be added in the near future. -
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RNA@
RNA annotation tool
...You will find at https://drive.google.com/file/d/1lEj5SSHpQSv54nOroxBcS_jvLFRIKNmm/view?usp=sharing" the RNA re-annotated by RNA@ for 30,558 genomes of Archaea and Bacteria (all the archaea and bacteria genomes marked as "Complete Genomes" or "Chromosome" among the genomes deposited in the NCBI day June 06 of 2021. You can also download the last version of the database at http://rnaat.ufpa.br -
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DSeg software
A MATLAB program to segment filamentous bacteria and hyphae structures
...Video instructions: https://www.youtube.com/embed/qMbM0shkk7A?rel Lastest updates: 20190930 DSeg: A dynamic segmentation program to extract backbone patterns for filamentous bacteria and hyphae structures,(2018). Hanqing Zhang,Niklas Soderholm, Linda Sandblad, Krister Wiklund, Magnus Andersson* -
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MetaAnnotator
Fast and Accurate Taxonomic Annotation for Metagenomic reads
...MetaAnnotator currently can not work on latest version of NCBI ref seq. I will update the program soon. You can use the archive version ftp://ftp.ncbi.nlm.nih.gov/genomes/archive/old_refseq/Bacteria/all.fna.tar.gz before that. Taxonomic annotation is a critical first step for analysis of metagenomic data. Despite a lot of tools being developed, the performance (both running time and accuracy) is still not satisfactory, in particular, when a close species-level reference does not exist in the database. we propose a novel annotation tool, MetaAnnotator, to annotate metagenomics reads which outperforms all existing tools significantly when only genus-level references exist in the database. -
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SML
SyntheticMicrobialLoop ; a model of phototroph-heterotroph interaction
Synthetic Microbial Loop - This project contains all the codes used to we have assemble a synthetic ecosystem to assist the systems-level investigation of diatom-bacteria biological association. The results obtained are described in https://www.biorxiv.org/content/early/2018/07/28/379131. -
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CRISPR-offinder-v1-2
A CRISPR tool for user-defined protospacer adjacent motif
...Target site cleavage by CRISPR technology requires a protospacer adjacent motif (PAM) immediately downstream or upstream of the protospacer element to which the sgRNA binds. However, Cas9 from different types of bacteria or variant recognizes different PAM sequences. To meet the needs of different CRISPR system with specific and efficient sgRNA design, CRISPR-offinder was developed. Given an input FASTA file of the target sites and queries the reference genome as well as a CRISPR system with a defined spacer length and PAM sequence, this standalone tool will identify putative sites and assign a predicted activity based on support vector machine model which conducted by sgRNA Scorer 2.0. ... -
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diauxic growth model ensemble
An ensemble of models showing diauxic growth behavior
An ensemble of mathematical model is presented that all show diauxic growth behaviour of a bacterial culture. Carbon catabolite repression (CCR) is the main mechanism controlling carbohydrate uptake in bacteria, and therefore also controlling whether or not different carbon sources are metabolized in parallel or sequentially. Although described as a paradigm of the regulation of bacterial metabolism, the underlying mechanisms remain controversial. The models in the ensemble can be categorized according to regulatory, stoichiometric, and physiological constraints and differ from each other on only a single aspect. ... -
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GenomeDatabase
For creating a local database of reference genomes
Genome Database - A tool to create a local database of reference genome sequences Usage: java path/to/GenomeDatabase.jar [options] By Marc Strous, 2016 This tool enables you to download fasta files of protein and RNA sequences encoded in reference genomes at NCBI. You can select relevant genomes with a set of queries. Each query has four fields, separated by comma's. Example of a queries are: superkingdom,Bacteria,genus,ftp superkingdom,Archaea,genus,ftp superkingdom,Eukaryota,phylum,ftp superkingdom,Viruses,family,elink The first query would download (with ftp) all available reference genomes of the superkingdom Bacteria, limited to one genome per genus. The second query would do the same for superkingdom Archaea. The third would download all Eukaryotic genomes, a single representative for each phylum. ... -
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MGplacer
Placer metagenomic data onto a phylogeny with 1000's of genomes
A rapid and robust method to identify lineage(s) of bacteria in metagenomic data, from a pre-defined phylogeny. Mixed-samples of multiple lineages in the phylogeny can be identified efficiently by iterately removal of assigned reads. -
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BRACIL-IA
Inference of Genome Accessibility in Bacteria from ChIP-seq data.
This code genome accessibility for transcription factor (TF)-binding in Bacteria. Transcription factors need physical access to DNA it can potentially bind. However, prior to this work it was impossible to measure and assess DNA accessibility in bacteria. This code uses ChIP-seq from multiple experiments to infer the hidden variable for genome accessibility. This is performed by a linear mixed effect model that considers two parameters: DNA affinity and DNA accessibility. ... -
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Genix: Bacterial Genome Annotation Pipel
A automated annotation pipeline for bacteria / archea genomes
Genix is an online automated pipeline for bacterial genome annotation that integrates the programs Prodigal, BLAST, RNAmmer, tRNAscan-SE, INFERNAL, ARAGORN and HMMER, and the databases Uniprot, Antifam and Rfam. -
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riboFR-seq
A novel approach to linking 16S rRNA amplicon profiles to metagenomes
...Here we propose a novel approach, RiboFR-Seq (Ribosomal RNA gene Flanking Region Sequencing), for capturing both ribosomal RNA variable regions and their flanking protein-coding genes simultaneously. We demonstrated that RiboFR-Seq could detect the vast majority of bacteria not only in well-studied microbiomes but also in novel communities with limited reference genomes. Combined with classical amplicon sequencing and shotgun metagenome sequencing, RiboFR-Seq can link the annotations of 16S rRNA and metagenomic contigs to make a consensus classification. -
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Shoal
A lot of fish in a shoal, in a gigantic scientific ocean.
Ours organization website GCModeller.org is coming online soon! Shoal Shell is the sub project for the "genome-in-code"(http://code.google.com/p/genome-in-code/) virtual cell modelling project of the bacteria Xcc 8004. Shoal Shell aim at provide the modelling tool and the debugging tool for the GCModeller virtual cell modelling, And from the extendible library package, shoal shell can manage to accomplish the entire modelling job for any other bacteria species. Shoal Shell Project needs grownup I'm just a student in the university, and the shoal shell just in its begining, if you have any idea about shoal, please contact me from xie.guigang@gmail.com. ... -
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COV2HTML
A visualization and analysis tool of Bacterial NGS data for Biologists
...(ii) COV2HTML, a visualization interface allowing a real-time analysis of data with selected criteria. Thus this interface offers a visualization of NGS mapping coverage data (DNA-seq, RNA-seq, ChIP-seq and TSS) performed in different prokaryotic organisms (bacteria, viruses...) or different experimental conditions (mutant versus wild type strains or different growth states…) facilitating studies. -
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Bactome
Tool box for studying bacteria, archae and complex taxons
Tool box for studying bacteria, archae and complex taxons -
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DNAcompact
Genome compression algorithm with/without reference (Linux/Windows)
...The proposed framework handles genome compression with and without reference seque- nces, and demonstrated performance advantage over the best existing algorithms. The proposed method without a reference led to bit rates of 1.720 and 1.838 bits per base for bacteria and yeast, which are approximately 3.7% and 2.6% better than the state-of-the-art algorithm. Regarding performance with reference, we tested on the first Korean personal genome sequence data set, and the proposed method demonstrated a 189-fold compression rate, reducing the raw file size from 2986.8 MB to 15.8 MB. -
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Image analysis program that extract the movements of the bacteria from digitised movies and data processing associated.
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The Application for GENetic Deviation Analysis (or AGENDA) allows users to genetically compare strains of a given bacteria to determine how mutated the bacteria has become.
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SimGen is Simulated Genetics. It simulates a simple DNA for moving within simple bacteria eating plankton. As good for Simulation it has Object-Oriented Design and is Coded in Java. It is a Applet and Dektop-Application and can be extended.
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This application is a useful tool to convert numeric series (chromatography or mass spectrometry) in a graphic, like SDS page gel or DNA gel to compare it visually. It also includes a database to quickly find matches with user defined profiles.
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Phage Therapy Simulation-Discrete Events
Discrete event model simulating bacteria and bacteriophage
Moved to: http://parkermills.github.io/phagetherapy/