ArticleNucleic acids research2017
Optimizing DNA assembly based on statistical language modelling.
Article in Nucleic acids research, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 3 papers.
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Who cites it
3 citing papers in PubMed.
- An Integrated Algorithm for Designing Oligodeoxynucleotides for Gene Synthesis.Frontiers in genetics · 2022Article
- Construction of a 3A system from BioBrick parts for expression of recombinant hirudin variants III in Corynebacterium glutamicum.Applied microbiology and biotechnology · 2020Article
- Scoring Amino Acid Mutations to Predict Avian-to-Human Transmission of Avian Influenza Viruses.Molecules (Basel, Switzerland) · 2018Article
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Authors and funding
3 authors.
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No grant is acknowledged in the PubMed record.
Abstract
By successively assembling genetic parts such as BioBrick according to grammatical models, complex genetic constructs composed of dozens of functional blocks can be built. However, usually every category of genetic parts includes a few or many parts. With increasing quantity of genetic parts, the process of assembling more than a few sets of these parts can be expensive, time consuming and error prone. At the last step of assembling it is somewhat difficult to decide which part should be selected. Based on statistical language model, which is a probability distribution P(s) over strings S that attempts to reflect how frequently a string S occurs as a sentence, the most commonly used parts will be selected. Then, a dynamic programming algorithm was designed to figure out the solution of maximum probability. The algorithm optimizes the results of a genetic design based on a grammatical model and finds an optimal solution. In this way, redundant operations can be reduced and the time and cost required for conducting biological experiments can be minimized.
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