Plasma dna manual

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PlasmaDNA:
a PLASmid MAnipulation program

2007, by Alexandre Angers-Loustau

Introduction
About the Program Plasma DNA is a free, cross-platform DNA manipulation program started in the end of 2006 by Dr Alexandre Angers-Loustau, a molecular biologist, while performing post-doctoral studies at the University of Helsinki. The aim of the program is to allow analysis and manipulation of DNAsequences in a simple and intuitive manner, targeting the everyday needs of scientists doing a lot of cloning and helping them keep track of the new sequences they produce. PlasmaDNA features: Full functionality on both Windows and MacOS operating systems, including compatibility of the saved files. Automatic analysis of DNA sequences for restriction sites, primer binding sites, and common plasmiddomains from easily-expandable (included) databases. Capacity to keep more than one sequence in the same file. Since PlasmaDNA keeps track of the overhangs of each fragment, this allows: In silico digestion with restriction enzymes, and ligation of compatible fragments to automatically generate the new sequences produced by reallife cloning. In silico Polymerase-Chain-Reaction (PCR). In silicoGATEWAY recombination between compatible fragments. Automatic determination of cloning strategies. Multiple sequence Import/Export compatibility with the FASTA format.

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License PlasmaDNA is a freeware, i.e. when you start it, you automatically agree to the following license: You are can use PlasmaDNA on as many computer computers as you like, for as long as you like,without charge. You are allowed, and encouraged, to distribute the program, provided that you distribute it as a complete package. This includes: -PlasmaDNA.exe (Windows) or PlasmaDNA.app (MacOS) -This manual, including this license -Enzymes.pdat -Domains.pdat -Primers.pdat -PlasmaDMan.exe (Windows) or PlasmaDMan.app (MacOS) -PlasmaDNA logo.png (Windows only) It is highly recommended to download a copydirectly from the author by going to the website http://research.med.helsinki.fi/plasmadna/. This program is provided by the author with the hope that it can be as useful to you as it is to himself. The author makes no guarantee, express or implied, of merchantability and fitness for a particular purpose, and can not be held responsible for direct or indirect damage, waste of material or wronginformation resulting from the use of this program. For feedback, questions, comments, or to report bugs, feel free to write me at http://research.med.helsinki.fi/plasmadna/Feedback/Feedback.htm/.

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Using PlasmaDNA
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1: Secondary windows show / hide. 2: Output window content selection. 3: Save / Export window. 4: Add a new fragment bytyping / pasting the sequence. 5: Add (a) new fragment(s) by importing from a FASTA-format file. 6: Load a file previously saved by PlasmaDNA. NOTE: the fragments in the loaded files will be ADDED to the fragments already present in the PlasmaDNA session. 7: Clear the current session. This deletes all the fragments and resets the program as if it just loaded. 8: Show/Hide the overlay of percent GCcontent of the DNA fragment. 9: Opens the “ About”window to see the current version number.

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10: Comments window. This allows to enter text that will be saved/loaded at the same time as the fragments. You can use this window to enter any kind of comments you would like to attach to the project. 11: Enzyme selection. This decides if the program uses all the enzymes present in the commercialenzymes database, or only those present in your laboratory. Restriction Enzyme Database: The enzyme database used by PlasmaDNA (Version 1.4 and later) comes from REBase (http://rebase.neb.com/rebase/rebase.files.html), and represents all the commercially available type II restriction enzymes (gtype2c.XXX, format #32). Updated version can be downloaded at any time, and added to the PlasmaDNA folder....
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