non-essential genes

[LDH-lin]

Hello,
When I use the local version of COPIES and run neutral site prediction with the example dataset s882c, the predicted sites do not overlap with non-essential genes. In fact, all predicted sites appear to avoid my gene regions entirely. Could you please explain why this happens?

Below is the command I used:
/data25/lindonghui/software/crispr/COPIES-main/code/main.py -g /data25/lindonghui/software/crispr/COPIES-main/data/s288c/GCF_000146045.2_R64_genomic.fna -t /data25/lindonghui/software/crispr/COPIES-main/data/s288c/GCF_000146045.2_R64_feature_table.txt -out /data25/lindonghui/other/02_caimiao/03_zhongxingweidian/06_s882c/s288c.new.csv -p NGG --intspace 400 --polyG_grna 4 --blast_org "Saccharomyces cerevisiae" --protein_file /data25/lindonghui/software/crispr/COPIES-main/data/s288c/GCF_000146045.2_R64_protein.faa

[aashutoshb97]

Hi,
In this work, we implemented CRISPR-COPIES specifically to identify intergenic regions suitable for heterologous gene integration. As described in the manuscript, heterologous integration has traditionally been performed at either intragenic or intergenic loci. However, intragenic integration necessarily disrupts an existing gene, which can impact cellular fitness.
Importantly, even disruption of non-essential genes may lead to unintended phenotypic effects, and gene essentiality itself is highly context- and environment-dependent. For these reasons, we deliberately focus on identifying and targeting intergenic regions, which minimizes the risk of perturbing native gene function.

As a result, when running COPIES in neutral site prediction mode (e.g., using the s882c example dataset), the predicted neutral sites are expected to avoid annotated gene regions, including non-essential genes. This behavior reflects the design of the workflow and the underlying assumptions used to prioritize intergenic loci as safer integration sites, rather than a limitation or error in the prediction.