| Title |
AAscan, PCRdesign and MutantChecker: A Suite of Programs for Primer Design and Sequence Analysis for High-Throughput Scanning Mutagenesis
|
|---|---|
| Published in |
PLOS ONE, October 2013
|
| DOI | 10.1371/journal.pone.0078878 |
| Pubmed ID | |
| Authors |
Dawei Sun, Martin K. Ostermaier, Franziska M. Heydenreich, Daniel Mayer, Rolf Jaussi, Joerg Standfuss, Dmitry B. Veprintsev |
| Abstract |
Scanning mutagenesis is a powerful protein engineering technique used to study protein structure-function relationship, map binding sites and design more stable proteins or proteins with altered properties. One of the time-consuming tasks encountered in application of this technique is the design of primers for site-directed mutagenesis. Here we present an open-source multi-platform software AAscan developed to design primers for this task according to a set of empirical rules such as melting temperature, overall length, length of overlap regions, and presence of GC clamps at the 3' end, for any desired substitution. We also describe additional software tools which are used to analyse a large number of sequencing results for the presence of desired mutations, as well as related software to design primers for ligation independent cloning. We have used AAscan software to design primers to make over 700 mutants, with a success rate of over 80%. We hope that the open-source nature of our software and ready availability of freeware tools used for its development will facilitate its adaptation and further development. The software is distributed under GPLv3 licence and is available at http://www.psi.ch/lbr/aascan. |
X Demographics
The data shown below were collected from the profiles of 4 X users who shared this research output. Click here to find out more about how the information was compiled.
Geographical breakdown
| Country | Count | As % |
|---|---|---|
| Netherlands | 1 | 25% |
| Unknown | 3 | 75% |
Demographic breakdown
| Type | Count | As % |
|---|---|---|
| Members of the public | 3 | 75% |
| Scientists | 1 | 25% |
Mendeley readers
The data shown below were compiled from readership statistics for 74 Mendeley readers of this research output. Click here to see the associated Mendeley record.
Geographical breakdown
| Country | Count | As % |
|---|---|---|
| Switzerland | 3 | 4% |
| Unknown | 71 | 96% |
Demographic breakdown
| Readers by professional status | Count | As % |
|---|---|---|
| Student > Bachelor | 15 | 20% |
| Researcher | 15 | 20% |
| Student > Ph. D. Student | 13 | 18% |
| Student > Master | 11 | 15% |
| Professor > Associate Professor | 3 | 4% |
| Other | 5 | 7% |
| Unknown | 12 | 16% |
| Readers by discipline | Count | As % |
|---|---|---|
| Agricultural and Biological Sciences | 23 | 31% |
| Biochemistry, Genetics and Molecular Biology | 21 | 28% |
| Chemistry | 4 | 5% |
| Medicine and Dentistry | 4 | 5% |
| Pharmacology, Toxicology and Pharmaceutical Science | 3 | 4% |
| Other | 7 | 9% |
| Unknown | 12 | 16% |