Search Results for "bacteria"

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:...

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. ...

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

...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. ...

...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.

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. ...

This project intends to create a bacteria simulator framework, with some realistic bacteria control methods based on chemical signaling, simple sensors, motors and neural networks. The bacteria will evolve in a genetic algorithm environment.

Image analysis program that extract the movements of the bacteria from digitised movies and data processing associated.

Moved to: http://parkermills.github.io/phagetherapy/

STARS is an alternative interface to staden for studying polymorphisms in short sequences with batch processing, manual editing, trace viewing and data management. STARS was initially designed for Multi Locus Sequence Typing of bacteria.