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MESA: automated assessment of synthetic DNA fragments and simulation of DNA synthesis, storage, sequencing and PCR errors
- Source :
- Bioinformatics
- Publication Year :
- 2020
- Publisher :
- Oxford University Press (OUP), 2020.
-
Abstract
- SummaryThe development of de novo DNA synthesis, polymerase chain reaction (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 article, 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.Availability and implementationMESA is available at mesa.mosla.de, with the source code available at github.com/umr-ds/mesa_dna_sim.Contactdominik.heider@uni-marburg.deSupplementary informationSupplementary data are available at Bioinformatics online.
- Subjects :
- Statistics and Probability
Computer science
Sequence analysis
Computational biology
Molecular cloning
Polymerase Chain Reaction
Biochemistry
DNA sequencing
Mesa
law.invention
03 medical and health sciences
chemistry.chemical_compound
0302 clinical medicine
law
Molecular Biology
Polymerase chain reaction
030304 developmental biology
computer.programming_language
Cloning
0303 health sciences
DNA synthesis
High-Throughput Nucleotide Sequencing
DNA
Sequence Analysis, DNA
Original Papers
Computer Science Applications
Computational Mathematics
Computational Theory and Mathematics
chemistry
Sequence Analysis
computer
Software
030217 neurology & neurosurgery
Subjects
Details
- ISSN :
- 14602059 and 13674803
- Volume :
- 36
- Database :
- OpenAIRE
- Journal :
- Bioinformatics
- Accession number :
- edsair.doi.dedup.....18543a7983fe8a6de794411fd5cf8154