CutSPR – Construction of Mutagenesis Vector based on the pJoe8999 plasmid system

CutSPR

:: DESCRIPTION

CutSPR is a bioinformatic tool for rapid primer design, and facilitates the cloning of specific CRISPR-Cas9-based mutagenesis plasmids.

::DEVELOPER

Göttingen Genomics Laboratory, Institut für Mikrobiologie and Genetik

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux / Windows/ MacOs
Python

:: DOWNLOAD

CutSPR

:: MORE INFORMATION

Citation

Schilling T, Dietrich S, Hoppert M, Hertel R.
A CRISPR-Cas9-Based Toolkit for Fast and Precise In Vivo Genetic Engineering of Bacillus subtilis Phages.
Viruses. 2018 May 4;10(5):241. doi: 10.3390/v10050241. PMID: 29734705; PMCID: PMC5977234.

HyAsP – Hybrid Assembler for Plasmids

HyAsP

:: DESCRIPTION

HyAsP is a tool for the extracting plasmids from WGS assemblies in an automatic way. It combines ideas from both reference-based and depth-based methods to identify plasmids in a greedy algorithm, using information on the occurrences of known plasmid genes and considering characteristics of the contigs such as read depth and GC content.

::DEVELOPER

Computational Methods for Paleogenomics and Comparative Genomics

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux
conda

:: DOWNLOAD

HyAsP

:: MORE INFORMATION

Citation

Müller R, Chauve C.
HyAsP, a greedy tool for plasmids identification.
Bioinformatics. 2019 Nov 1;35(21):4436-4439. doi: 10.1093/bioinformatics/btz413. PMID: 31116364.

Bakta 1.2.2 – Rapid & Standardized Annotation of Bacterial Genomes & Plasmids

Bakta 1.2.2

:: DESCRIPTION

Bakta is a tool for the rapid & standardized annotation of bacterial genomes & plasmids.

::DEVELOPER

Bioinformatics and Systems Biology, Justus-Liebig-University

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux

:: DOWNLOAD

Bakta

:: MORE INFORMATION

Citation

Schwengers O, Jelonek L, Dieckmann MA, Beyvers S, Blom J, Goesmann A.
Bakta: rapid and standardized annotation of bacterial genomes via alignment-free sequence identification.
Microb Genom. 2021 Nov;7(11). doi: 10.1099/mgen.0.000685. PMID: 34739369.

COPLA – Taxonomic Classifier of Plasmids

COPLA

:: DESCRIPTION

COPLA is an application for plasmid classification in Plasmid Taxonomic Units (PTUs).

:: DEVELOPER

irycis Bioinfo

:: REQUIREMENTS

Linux / Window
Perl

:: DOWNLOAD

COPLA

:: MORE INFORMATION

Citation

Redondo-Salvo S, Bartomeus-Peñalver R, Vielva L, Tagg KA, Webb HE, Fernández-López R, de la Cruz F.
COPLA, a taxonomic classifier of plasmids.
BMC Bioinformatics. 2021 Jul 31;22(1):390. doi: 10.1186/s12859-021-04299-x. PMID: 34332528; PMCID: PMC8325299.

PLACNET 1.04 / PLACNETw – Plasmid Constellation Network project

PLACNET 1.04 / PLACNETw

:: DESCRIPTION

PLACNET is a graph-based tool for reconstruction of plasmids from next generation sequence pair-end datasets.

PLACNETw, a web tool based on PLACNET, provides an interactive graphic interface, automates BLAST searches, and extracts the relevant information for decision making.

:: DEVELOPER

irycis Bioinfo

:: REQUIREMENTS

Linux / Window
Python

:: DOWNLOAD

PLACNET / PLACNETw

:: MORE INFORMATION

Citation

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 Dec 18;10(12):e1004766. doi: 10.1371/journal.pgen.1004766. PMID: 25522143; PMCID: PMC4270462.

Vielva L, de Toro M, Lanza VF, de la Cruz F.
PLACNETw: a web-based tool for plasmid reconstruction from bacterial genomes.
Bioinformatics. 2017 Dec 1;33(23):3796-3798. doi: 10.1093/bioinformatics/btx462. PMID: 29036591.

PlasmaDNA 1.4.2 – PLAsmid MAnipulation program

PlasmaDNA 1.4.2

:: DESCRIPTION

PlasmaDNA is a new, free DNA analysis and manipulation software. It is simple to learn and to use, and contains multiple features designed to help with:

The design of a successful cloning strategy
The generation of the sequences of new clones
The archiving of the cloning strategy

::DEVELOPER

Alexandre Angers-Loustau, Ph.D.
+358 9 191 25142
Haartmaninkatu 8
alexandre.angers-loustau (at) helsinki.fi

:: SCREENSHOTS

:: REQUIREMENTS

Windows / Mac OsX

:: DOWNLOAD

PlasmaDNA

:: MORE INFORMATION

Citation:

Alexandre Angers-Loustau , Jeffrey Rainy and Kirmo Wartiovaara
PlasmaDNA: a free, cross-platform plasmid manipulation program for molecular biology laboratories
BMC Molecular Biology 2007, 8:77

ApE 3.0.3 – A Plasmid Editor

ApE 3.0.3

:: DESCRIPTION

ApE (A Plasmid Editor) is an integrated program for plasmid construction and visualization. It includes a sequence editor, a linear text map identifying sequence features such as restriction sites and ORFs, and a graphic view that highlights sites and features in your sequences. A program designed by a molecular biologist, for molecular biologists.

::DEVELOPER

M. Wayne Davis

:: SCREENSHOTS

:: REQUIREMENTS

MacOsX / Windows / Linux
Tcl/Tk

:: DOWNLOAD

ApE

:: MORE INFORMATION

GenoCAD 2.3.1 – Design of Plasmids and Synthetic DNA Sequences

GenoCAD 2.3.1

:: DESCRIPTION

GenoCAD is an open-source computer-assisted-design (CAD) application for synthetic biology. The foundation of GenoCAD is to consider DNA as a language to program synthetic biological systems.

::DEVELOPER

GenoCAD team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Web Browser

:: DOWNLOAD

GenoCAD

:: MORE INFORMATION

Citation

Writing DNA with GenoCAD.
Czar MJ, Cai Y, Peccoud J.
Nucleic Acids Res. 2009 Jul;37(Web Server issue):W40-7. doi: 10.1093/nar/gkp361

FindPlasmids 20180522 – Find plasmids in Microbial Genome Assembly Files

FindPlasmids 20180522

:: DESCRIPTION

FindPlasmids identifies known plasmids in genome assembly files by using the assembly file to query a local Blast+ database of plasmid sequences.

::DEVELOPER

Barry G. Hall

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Windows/Linux/MacOsX

:: DOWNLOAD

FindPlasmids

:: MORE INFORMATION

BVTech Plasmid 5.1 – DNA Sequence Analysis & Plasmid Drawing Software

BVTech Plasmid 5.1

:: DESCRIPTION

BVTech Plasmid is DNA sequence analysis and plasmid drawing software for Windows PCs. You can use it to plan your DNA cloning, draw high quality plasmid maps, analyse your DNA sequencing data, align sequences, and much more. BVTech Plasmid is easy to use, powerful, and affordable for molecular biologists at any level.

::DEVELOPER

BVTech, Inc.

:: SCREENSHOTS

:: REQUIREMENTS

Windows

:: DOWNLOAD

BVTech Plasmid Demo

:: MORE INFORMATION

Registration of BVTech Plasmid