ArticleBioinformatics (Oxford, England)2019
High-complexity regions in mammalian genomes are enriched for developmental genes.
Article in Bioinformatics (Oxford, England), 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. An erratum has been issued. Cited by 9 papers.
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Who cites it
9 citing papers in PubMed.
- Seqwin: Ultrafast identification of signature sequences in microbial genomes.bioRxiv : the preprint server for biology · 2025Article
- Unbiased anchors for reliable genome-wide synteny detection.Algorithms for molecular biology : AMB · 2025Article
- Detection and annotation of unique regions in mammalian genomes.G3 (Bethesda, Md.) · 2025Article
- Fast detection of unique genomic regions.Computational and structural biotechnology journal · 2025Review
- Fast, parallel, and cache-friendly suffix array construction.Algorithms for molecular biology : AMB · 2024Article
- Fine-Scale Map Reveals Highly Variable Recombination Rates Associated with Genomic Features in the Eurasian Blackcap.Genome biology and evolution · 2024Article
- Marker discovery in the large.Bioinformatics advances · 2024Article
- Bioinformatics tools for the sequence complexity estimates.Biophysical reviews · 2023Review
- Fur: Find unique genomic regions for diagnostic PCR.Bioinformatics (Oxford, England) · 2021Article
Corrections and comments
- Erratum issued
Authors and funding
4 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
motivationUnique sequence regions are associated with genetic function in vertebrate genomes. However, measuring uniqueness, or absence of long repeats, along a genome is conceptually and computationally difficult. Here we use a variant of the Lempel-Ziv complexity, the match complexity, Cm, and augment it by deriving its null distribution for random sequences. We then apply Cm to the human and mouse genomes to investigate the relationship between sequence complexity and function.
resultsWe implemented Cm in the program macle and show through simulation that the newly derived null distribution of Cm is accurate. This allows us to delineate high-complexity regions in the human and mouse genomes. Using our program macle2go, we find that these regions are twofold enriched for genes. Moreover, the genes contained in these regions are more than 10-fold enriched for developmental functions. AVAILABILITY AND IMPLEMENTATION: Source code for macle and macle2go is available from www.github.com/evolbioinf/macle and www.github.com/evolbioinf/macle2go, respectively; Cm browser tracks from guanine.evolbio.mgp.de/complexity. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
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