Search Results for "plasmid"

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.

...It uses a nested membrane-surroundings entitites scheme formatted in a XML file. The created scenarios emulate entities as: i) Resistance genes, able to detoxify antibiotics. These genes can be located in the plasmid, in conjugative elements or in the chromosome; ii) plasmids and conjugative elements transferring genes between bacterial cells; iii) bacterial cells; iv) individual microbiotas where bacterial species coexist; v) hosts containing the microbiotic ensembles; vi) environment(s) where the hosts are contained. Our model facilitates the simultaneous analysis of several features of interest in the prediction of the rules governing the multi-level evolutionary biology of antibiotic resistance, according to a set of pre-established rules. ...

...It also designs synonymous codon fragments required to manipulate essential target genes to enable survival of the strain during the genome editing procedure. GetX provides genbank and fasta format files for a mutation template plasmid, a mutation cassette, and a sequence around the mutation site to guide the user through the design of the materials required for the scarless bacterial genome editing method.

...Placnet obtains a set of files, easily opened on Cytoscape software or other network tools. Please cite PLACNET as: Lanza VF, de Toro M, Garcillán-Barcia MP, Mora A, Blanco J, Coque TM, de la Cruz F: Plasmid Flux in Escherichia coli ST131 Sublineages, Analyzed by Plasmid Constellation Network (PLACNET), a New Method for Plasmid Reconstruction from Whole Genome Sequences. PLoS Genet 2014, 10:e1004766.

Plasmid designer (PlaNer) is a software developed to easily create plasmid maps and extract the figure of it. Features, that is 'genes' (i.e. sequences of interest) or 'sites' (e.g. restriction sites), can be added, removed or deleted at any time. For every Feature, a different colour can be determined for appropriate visualization. The list of the features can be saved at any time and an existing one can be loaded to continue configuring a previously saved plasmid map. ...

A GUI program to create the plasmid database forms for BGME lab. This program presents user with a data entry form for entering plasmid information and automatically converts DNA sequence to protein, aligns it, and creates text output file.

Easy install web server for Genetic and Molecular Biological Laboratory so that PI can update lab homepage himself. Also serve as Lab database server that store DNAStrider plasmid , order tracking and mouse colony database.

A peer-to-peer file replication (synchronization) engine written in Java. Managed via the web. Keywords: RMI, JSP, Sync, P2P.