Graphical representation of DNA sequences provides a simple and intuitive way of viewing, anchoring, and comparing various gene structures, so a simple and non-degenerate method is attractive to both biologists and computational biologists. In this study, a universal graphical representation method for DNA sequences based on S.S.-T. Yau's method is presented. The method adopts a trigonometric function to represent the four nucleotides A, G, C, and T. Some interesting characteristics of the universal representation are introduced. We exploit frequency analysis with our representation method on DNA sequences, demonstrating possible applications in coding region prediction, and sequence analysis. Based on the statistically experimental results from this frequency analysis, a simple coding region predictor and an optimized one are presented. An experiment on the broadly accepted ROSETTA data set demonstrates that the performance of the optimized predictor is comparable to that of other popular methods.
Download full-text PDF |
Source |
|---|---|
| http://dx.doi.org/10.1089/cmb.2008.0041 | DOI Listing |
Publication Analysis
Top Keywords
Similar Publications
Impaired spatial coding of the hippocampus in a dentate gyrus hypoplasia mouse model.
Proc Natl Acad Sci U S A
February 2025
Zanvyl Krieger Mind/Brain Institute, Johns Hopkins University, Baltimore, MD 21218.
The hippocampal dentate gyrus (DG) is thought to orthogonalize inputs from the entorhinal cortex (pattern separation) and relay this information to the CA3 region. In turn, attractor dynamics in CA3 perform a pattern completion or error correction operation before sending its output to CA1. In a mouse model of congenital hypoplasia of the DG, a deficiency in the (Wls) gene, specifically in cells expressing , which targets neuronal progenitors, led to an almost total absence of dentate granule cells and modestly impaired performance in spatial tasks.
View Article and Find Full Text PDFHippocampal coding of identity, sex, hierarchy, and affiliation in a social group of wild fruit bats.
Science
January 2025
Department of Brain Sciences, Weizmann Institute of Science, Rehovot, Israel.
Social animals live in groups and interact volitionally in complex ways. However, little is known about neural responses under such natural conditions. Here, we investigated hippocampal CA1 neurons in a mixed-sex group of five to 10 freely behaving wild Egyptian fruit bats that lived continuously in a laboratory-based cave and formed a stable social network.
View Article and Find Full Text PDFViroids, small circular non-coding RNAs, act as infectious pathogens in higher plants, demonstrating high stability despite consisting solely of naked RNA. Their dependence of replication on host machinery poses the question of whether RNA modifications play a role in viroid biology. Here, we explore RNA modifications in the avocado sunblotch viroid (ASBVd) and the citrus exocortis viroid (CEVd), representative members of viroids replicating in chloroplasts and the nucleus, respectively, using LC - MS and Oxford Nanopore Technology (ONT) direct RNA sequencing.
View Article and Find Full Text PDFFungal-derived tRNAs are expressed and aminoacylated in orchid mitochondria.
Mol Biol Evol
January 2025
Department of Biology, Colorado State University, Fort Collins, CO, USA.
Plant mitochondrial genomes (mitogenomes) experience remarkable levels of horizontal gene transfer (HGT), including the recent discovery that orchids anciently acquired DNA from fungal mitogenomes. Thus far, however, there is no evidence that any of the genes from this interkingdom HGT are functional in orchid mitogenomes. Here, we applied a specialized sequencing approach to the orchid Corallorhiza maculata and found that some fungal-derived tRNA genes in the transferred region are transcribed, post-transcriptionally modified, and aminoacylated.
View Article and Find Full Text PDFMulti-sample long-read nanopore sequencing of Agabus bipustulatus (Coleoptera: Dytiscidae: Agabinae) mitogenome produces effectively reliable data for downstream analyses.
J Insect Sci
January 2025
ZooLab, Department of Biodiversity and Ecology, Plant Science and Biodiversity Centre, Slovak Academy of Sciences, Bratislava, Slovakia.
Mitochondrial genomes are a rich source of data for various downstream analyses such as population genetics, phylogeny, and systematics. Today it is possible to assemble rapidly large numbers of mitogenomes, mainly employing next-generation sequencing and third-generation sequencing. However, verification of the correctness of the generated sequences is often lacking, especially for noncoding, length-variable parts.
View Article and Find Full Text PDFWant AI Summaries of new PubMed Abstracts delivered to your In-box?
Enter search terms and have AI summaries delivered each week - change queries or unsubscribe any time!