Build Step: Plasmid Construction Services
Plasmid construction data services have roots in previously published applications including GeneDesign and GenoREAD.
These data service support the Build step of the DBLT cycle by implementing workflows based on Gibson assembly or other assembly technologies. Plasmid construction is enabling the design of new plasmids and optimization of expression vectors. GenoCAM supports the assembly of plasmids designed using the design services.
These scripts have several original features:
- They have an API making possible to integrate them into automated workflows. and connect them to suppliers.
- They support high-throughput operations.
- They rely on complex bioinformatics pipeline tuned to achieve a particular objective in a predictable way.
Plasmid Construction Scripts
These scripts are scripts focused on preparing the orders for assembling synthetic DNA fragments
- Build Blocks: Breaks down a long DNA sequence into smaller fragments that may be overlapping or not. This step is necessary because it is not possible to order or synthesize long DNA molecules. They need to be assembled from smaller fragments.
- PCA Oligo Design: This script would take blocks generated by 1 and break them down further into a set of overlapping oligos. This is for people who may be interested in doing the gene synthesis in house. In practice, it is not cost effective to do that any more.
- Assess GC Content: This script would take the output of 1 and detect regions of high gc content that are predictive of synthesis problems.
- PCR Primers Script: The goal of this script is to design PCR primers that make it possible to amplify a series (96) of DNA fragments using the same amplification profile. The PCR primers can have a common set of overhanging complementary of the vector where the PCR fragment will be inserted. They can also have different overhangs in situations where each PCR product is inserted in a different plasmid as in the iVector project.
Plasmid Verification Scripts
These are scripts streamlining the quality control step at the end of the DNA assembly process
- Sanger Sequencing Primer Design: This script takes the sequence or one plasmid or multiple plasmids as input and produces a set of sequencing primers that provide between 1x and 2x coverage of the entire plasmid.
- Sequence Verification Using Sanger Sequencing: This script takes a series of Sanger sequencing reads and a plasmid theoretical sequence as input, aligns the reads to the theoretical sequences, and compares the read assembly with the reference sequence.
- Sequence Verification Using Illumina Sequencing: This script takes a series of short reads as input, performs a de novo assembly, and analyzes the quality of the assembly, and compare it to a reference sequence.
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