Evidence map›Paper›PMID 39717051›Full record

ArticlePeerJ2024

Visual codon: a user-friendly Python program for viewing and optimizing gene GC content.

Shiming Lin, Fei Xu, Bifang Huang, Li-Li Zhao, Danni Pan, Shiqiang Lin

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in PeerJ, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 1 paper.

0numbers the graph read from it
0cells of the map it votes in
1citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

1 citing paper in PubMed.

  1. Article
4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

6 authors.

Shiming Lin *School of Computing and Information Science, Fuzhou Institute of Technology, Fuzhou, Fujian, China.
Fei Xu *College of Agronomy, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China.
Bifang HuangLife Science College, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China.
Li-Li ZhaoNational Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China.
Danni PanCollege of Agronomy, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China.
Shiqiang LinLife Science College, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China.ORCID 0000-0001-7181-4261

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

Due to the codon bias of different species, codon optimization is usually carried out in the process of heterologous protein expression. At present, there are a variety of codon optimization tools. However, the optimized sequences may still have high or low points of local guanine and cytosine (GC) content, which is not conducive to the primer design of gene subcloning, and also makes it difficult to perform the experiment of synthesizing the whole gene with DNA fragments by polymerase chain reaction (PCR) reaction. In this study, we present a stand-alone software written in Python, with which users can manually check and adjust the GC content of sequence-optimized genes. The software takes the codon frequency of

Indexed as

Base CompositionCodonEscherichia coliSoftwareUser-Computer InterfaceCodonCodon optimizationGC contentGene synthesisPythonSubcloning

Identifiers

PMID39717051
PMCPMC11665431

What OpenQuestion holds

Textmetadata
LicenceCC BY
Read underepoch 390

Registered trials

None linked

Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.