Search Results for "bacteria"
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Showing 42 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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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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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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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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MicrobialChemostatSimulation
Computer Lesson and Simulation of Bacterial Chemostat and Chemotaxis
CheStatGen2b.exe will install a Lesson and Simulation of Bacterial Motility and Chemotaxis in a Chemostat Simulation. Bacterial Chemotaxis is the motion up or down the direction of an attractant or repelant of each bacteria. The simulation also demonstrates the bacterial mechanism of this utility. The Lesson also gives the Microbiology used in the simulation. It is coded in vb.net in MS Visual Studio 2022 Please note: After downloading and running the CheStatGen2b.exe file, also run the Setup file in the c:\Users\Public\CheStatGen2b directory. ... -
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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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BacterialChemotaxis
Computer Lesson and Simulation of Bacterial Chemotaxis
CSim3a.exe will install a Lesson and Simulation of Bacterial Chemotaxis. Bacterial Chemotaxis is the motion up or down the direction of an attractant or repelant of each bacteria. The simulation also demonstrates the bacterial mechanism of this utility. The Lesson also gives the Basic code used in the simulation. Installs as motility3a in c:/users/public/CSim3a -
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GLUVAB
Genomic Lineages of Uncultured Viruses of Archaea and Bacteria
Perl script that automates the analyses to establish GL-UVAB (Genomic Lineages of Uncultured Viruses of Archaea and Bacteria). These include: 1) Identification of protein encoding genes with Prodigal. 2) All-versus-all protein search with Diamond. 3) Calculating Dice distances. 4) Building Dice tree using R 5) Identifying lineages based on the user defined criteria. -
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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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Extract 16S rRNA from genomes
This script extracts 16S rRNA sequences from multifasta files
...The HMM files arc.ssu.rnammer.hmm and bac.ssu.rnammer.hmm have to be in the same software were executable file is saved. Inside the folder creates two sub-folders named "bacteria" and "archaea" where you will save your multifasta files (multifasta of bacteria in one and of archaea in the other one). MORE DETAILS IN THE FILE INCLUDED... -
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Microbial Genomics Tools
MGT is Codon usage analysis tool
...Kishor Shende (Information Officer), at Bioinformatics Center, barkatullah University. This software is attributed as - 1. Microbial Genomic Tool (MGT 1.0), the first version is developed for In-silico research bacteria genomic study and useful for the Students and research scholars working in the field of Microbial Genomics. 2. User-friendly graphical interface 3. It provides application for calculation of codon frequency, RSCU, AT3, GC3, Nc Enc, nucleotide composition and percent values. 4. Result can be viewed in MS-Excel sheet. 5. MGT development was initiated with the future intention to provide multi-application software for bacterial genome analysis. -
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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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GetX
An automated mutation cassette design tool for scarless genome editing
We developed GetX, a stand-alone python script that allows the user to design mutation cassettes for scarless genome editing in bacteria using our previously described two-step recombination method. GetX allows the user to design synthetic DNA fragments required to perform bacterial genome editing with simple inputs of 1) genome information from the target strain and 2) information for the desired mutation. GetX designs DNA fragments for introduction of sequences for protein tagging, deletions, insertions, and point mutations. ... -
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TAL evolution scripts
Scripts to assess TAL effector diversity and find evolutionary pattern
TAL effectors (aka TALEs) are repeat containing proteins found in the genus of phytopathogenic bacteria Xanthomonas. They are able to bind DNA through their repeat region and induce genes in the host plant. Thus variation in repeat number and order can lead to diversification of virulence functions and evasion of recognition by the host. Variation in TAL effector repeats and repeat sequence between different taxonomic groups has remained largely unexplored. -
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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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This project includes perl scripts to perform transcriptome reconstruction in bacteria (operons and UTRs). The software was applied to the transcriptome reconstruction of the species Methanococcoides burtonii, if you use it please refer to the following paper (Taha et al., Single TRAM domain RNA-binding proteins in Archaea: functional insights from Ctr3 from the Antarctic methanogen Methanococcoides burtonii - Submitted).
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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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Cosci 1336-261project
This program determines which bacteria are to be used in diagnotics.
This program reads a file called, "Data-Project-1.txt" and determines the average bacteria population of healthy subjects and diseased subjects. It then determines which bacteria will be used to diagnose subjects in a second file called, "Data-Project-2.txt" At the end, it will print out which subjects are considered diseased or healthy. -
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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. ...
