MESA: automated assessment of synthetic DNA fragments and simulation of DNA synthesis, storage, sequencing, and PCR errors

Bioinformatics
Michael SchwarzDominik Heider

Abstract

The development of de novo DNA synthesis, PCR, DNA sequencing, and molecular cloning gave researchers unprecedented control over DNA and DNA-mediated processes. To reduce the error probabilities of these techniques, DNA composition has to adhere to method-dependent restrictions. To comply with such restrictions, a synthetic DNA fragment is often adjusted manually or by using custom-made scripts. In this paper, we present MESA (Mosla Error Simulator), a web application for the assessment of DNA fragments based on limitations of DNA synthesis, amplification, cloning, sequencing methods, and biological restrictions of host organisms. Furthermore, MESA can be used to simulate errors during synthesis, PCR, storage, and sequencing processes. MESA is available at mesa.mosla.de, with the source code available at github.com/umr-ds/mesa_dna_sim. Supplementary data are available at Bioinformatics online.

References

Oct 21, 1998·Journal of Theoretical Biology·K J Dawson
May 31, 2007·BMC Bioinformatics·Dominik Heider, Angelika Barnekow
Apr 23, 2008·BMC Molecular Biology·Dominik Heider, Angelika Barnekow
Jul 5, 2008·Bioinformatics·Dominik HeiderAngelika Barnekow
Jul 9, 2009·BMC Research Notes·Dominik HeiderAngelika Barnekow
Mar 17, 2010·BMC Bioinformatics·Jessica S Reuter, David H Mathews
Jun 24, 2010·BioTechniques·Aron FazekasSteven Newmaster
Sep 20, 2012·Proceedings of the National Academy of Sciences of the United States of America·Heewook LeePatricia L Foster
May 2, 2014·Nature Methods·Sriram Kosuri, George M Church
Sep 10, 2014·Molecular Biology International·Peter McInerneyMasood Z Hadi
May 31, 2015·Briefings in Bioinformatics·David LaehnemannAlice Carolyn McHardy
Mar 13, 2016·BMC Bioinformatics·Melanie SchirmerChristopher Quince
Jun 19, 2016·G3 : Genes - Genomes - Genetics·Way SungMichael Lynch
May 10, 2019·Nature Reviews. Genetics·Luis CezeKarin Strauss

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Citations

May 22, 2021·Frontiers in Genetics·Yanfen ZhengBin Wang
Aug 19, 2021·BMC Bioinformatics·Peter Michael Schwarz, Bernd Freisleben

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Methods Mentioned

BETA
PCR

Software Mentioned

RNAStructure
Docker
PHRED
PostgreSQL
MESA
MESA ( Mosla Error Simulator )

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