CodingDiv: analyzing SNP-level microdiversity to discriminate between coding and noncoding regions in viral genomes.
basic_science · Level V
Where this comes from
- Record sourced from PubMed, PMID 37449883.
- Also identified by DOI 10.1093/bioinformatics/btad408 and PMC identifier 10356776.
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Abstract
Viral genes, that are frequently small genes and/or with large overlaps, are still difficult to predict accurately. To help predict all genes in viral genomes, we provide CodingDiv that detects SNP-level microdiversity of all potential coding regions, using metagenomic reads and/or similar sequences from external databases. Protein coding regions can then be identified as the ones containing more synonymous SNPs than unfavorable nonsynonymous substitutions SNPs. CodingDiv is released under the GPL license. Source code is available at https://github.com/ericolo/codingDiv. The software can be installed and used through a docker container.
Medical subject headings
- Polymorphism, Single Nucleotide
- Software