Background: Gene finding is a complicated procedure that encapsulates algorithms for coding sequence modeling, identification of promoter regions, issues concerning overlapping genes and more. In the present study we focus on coding sequence modeling algorithms; that is, algorithms for identification and prediction of the actual coding sequences from genomic DNA. In this respect, we promote a novel multivariate method known as Canonical Powered Partial Least Squares (CPPLS) as an alternative to the commonly used Interpolated Markov model (IMM). Comparisons between the methods were performed on DNA, codon and protein sequences with highly conserved genes taken from several species with different genomic properties.
Results: The multivariate CPPLS approach classified coding sequence substantially better than the commonly used IMM on the same set of sequences. We also found that the use of CPPLS with codon representation gave significantly better classification results than both IMM with protein (p < 0.001) and with DNA (p < 0.001). Further, although the mean performance was similar, the variation of CPPLS performance on codon representation was significantly smaller than for IMM (p < 0.001).
Conclusions: The performance of coding sequence modeling can be substantially improved by using an algorithm based on the multivariate CPPLS method applied to codon or DNA frequencies.
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http://dx.doi.org/10.1186/1471-2105-13-97 | DOI Listing |
BMC Genom Data
January 2025
Department of Applied Biosciences, College of Agriculture and Life Sciences, Kyungpook National University, Daegu, 41566, Republic of Korea.
Objectives: The data were collected to obtain the complete genome sequence of Pseudarthrobacter sp. NIBRBAC000502770, isolated from the rhizosphere of Sasamorpha in a heavy metal-contaminated coal mine in Hongcheon, Republic of Korea. The objective was to explore the strain's genetic potential for plant growth promotion and heavy metal resistance, particularly arsenate and copper.
View Article and Find Full Text PDFJ Neurosci
January 2025
Department of Physiology, University of Maryland School of Medicine, Baltimore, MD, USA
The cell adhesion molecule Leucine-Rich Repeat Transmembrane neuronal protein 2 (LRRTM2) is crucial for synapse development and function. However, our understanding of its endogenous trafficking has been limited due to difficulties in manipulating its coding sequence (CDS) using standard genome editing techniques. Instead, we replaced the entire LRRTM2 CDS by adapting a two-guide CRISPR knock-in method, enabling complete control of LRRTM2.
View Article and Find Full Text PDFJ Glob Antimicrob Resist
January 2025
Clinical Laboratory Department, Lishui People's Hospital, the Sixth Affiliated Hospital of Wenzhou Medical University, Lishui, China. Electronic address:
Objectives: Pandoraea apista is notable for its multidrug resistance and is frequently identified in patients with cystic fibrosis or other chronic lung diseases, where it contributes to persistent lung infections. In this study, we describe a strain of P. apista harboring the bla, isolated from the bronchoalveolar lavage (BAL) fluid of an inpatient in China.
View Article and Find Full Text PDFWellcome Open Res
November 2024
UK Centre for Ecology & Hydrology, Wallingford, England, UK.
We present a genome assembly from an individual male (Poplar Grey moth; Arthropoda; Insecta; Lepidoptera; Noctuidae). The genome sequence has a total length of 424.20 megabases.
View Article and Find Full Text PDFArch Virol
January 2025
School of Agriculture, Utsunomiya University, 350 Mine-machi, Utsunomiya, Tochigi, 321-8505, Japan.
Tulip mild mottle mosaic disease, caused by tulip mild mottle mosaic virus (TMMMV, species Ophiovirus tulipae), was first reported in Japan in 1979. TMMMV has a negative-sense ssRNA genome and is closely related to ophioviruses such as Mirafiori lettuce big vein virus (MLBVV, Ophiovirus mirafioriense). However, its complete nucleotide sequence has not yet been reported.
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