Difference between revisions of "User:Chris D Hirst/Plasma"

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m (New page: ==Introduction== PlasmaDNA<cite>#1</cite> is a free to use computer programme developed by the University of Helsinki to allow the easy mainpulation of DNA ''in silico''. In the hands of ...)
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Revision as of 04:04, 5 July 2010

Introduction

PlasmaDNA[1] is a free to use computer programme developed by the University of Helsinki to allow the easy mainpulation of DNA in silico. In the hands of an experience user, it can be used to fully plan out the assembly of a synthetic construct from base parts, genome sequences, cDNAs - basically any DNA input for which a text or FASTA file can be found. The ability to attempt a cloning strategm in silico before going into the lab can help identify bottlenecks and critical paths while allowing the user to visually see what they are producing.

While other programmes can do this, PlasmaDNA is free, very use friendly and produces highly detailed plasmid maps in 3 flavours. Some lab members already create PlasmaDNA (.pof) files for all teh vectors and constructs they build. This and the ability to visualise cloning can prove very useful to aid understanding and debug when issues arise.

PlasmaDNA can be accessed here.

Tutorial

Importing

Restriction Enzyme, ORF and Primer Binding Analysis

Cloning - Biobricks RFC 10 (BBa)

Analysis of cloning results

Cloning - PCR and Biobrick (BBa)

Cloning - Infusion

Exporting

References

  1. Angers-Loustau A, Rainy J, and Wartiovaara K. PlasmaDNA: a free, cross-platform plasmid manipulation program for molecular biology laboratories. BMC Mol Biol. 2007 Sep 17;8:77. DOI:10.1186/1471-2199-8-77 | PubMed ID:17868482 | HubMed [1]