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Investigating the evolutionary dynamics of diploid number variation in Ctenomys (Ctenomyidae, Rodentia). 研究栉水母(栉水母科,啮齿目)二倍体数量变异的进化动态。
IF 2.1 4区 生物学
Genetics and Molecular Biology Pub Date : 2024-02-05 eCollection Date: 2024-01-01 DOI: 10.1590/1678-4685-GMB-2023-0180
Thays Duarte de Oliveira, Thales R O de Freitas
{"title":"Investigating the evolutionary dynamics of diploid number variation in Ctenomys (Ctenomyidae, Rodentia).","authors":"Thays Duarte de Oliveira, Thales R O de Freitas","doi":"10.1590/1678-4685-GMB-2023-0180","DOIUrl":"10.1590/1678-4685-GMB-2023-0180","url":null,"abstract":"<p><p>Contrary to predictions from classical hybrid sterility models of chromosomal speciation, some organisms display high rates of karyotype variation. Ctenomys are the current mammals with the greatest interspecific and intraspecific chromosomal variation. A large number of species have been studied cytogenetically. The diploid numbers of chromosomes range from 2n = 10 to 2n = 70. Here, we analyzed karyotype evolution in Ctenomys using comparative phylogenetic methods. We found a strong phylogenetic signal with chromosome number. This refutes the chromosomal megaevolution model, which proposes the independent accumulation of multiple chromosomal rearrangements in each closely related species. We found that Brownian motion (BM) described the observed characteristic changes more thoroughly than the Ornstein-Uhlenbeck and Early-Burst models. This suggests that the evolution of chromosome numbers occurs by a random walk along phylogenetic clades. However, our data indicate that the BM model alone does not fully characterize the chromosomal evolution of Ctenomys.</p>","PeriodicalId":12557,"journal":{"name":"Genetics and Molecular Biology","volume":"46 3 Suppl 1","pages":"e20230180"},"PeriodicalIF":2.1,"publicationDate":"2024-02-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10842476/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139691632","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
DOF gene family expansion and diversification. DOF 基因家族的扩展和多样化。
IF 2.1 4区 生物学
Genetics and Molecular Biology Pub Date : 2024-02-05 eCollection Date: 2024-01-01 DOI: 10.1590/1678-4685-GMB-2023-0109
Edgar Luis Waschburger, João Pedro Carmo Filgueiras, Andreia Carina Turchetto-Zolet
{"title":"DOF gene family expansion and diversification.","authors":"Edgar Luis Waschburger, João Pedro Carmo Filgueiras, Andreia Carina Turchetto-Zolet","doi":"10.1590/1678-4685-GMB-2023-0109","DOIUrl":"10.1590/1678-4685-GMB-2023-0109","url":null,"abstract":"<p><p>DOF (DNA binding with one finger) proteins are part of a plant-specific transcription factor (TF) gene family widely involved in plant development and stress responses. Many studies have uncovered their structural and functional characteristics in recent years, leading to a rising number of genome-wide identification study approaches, unveiling the DOF family expansion in angiosperm species. Nonetheless, these studies primarily concentrate on particular taxonomic groups. Identifying DOF TFs within less-represented groups is equally crucial, as it enhances our comprehension of their evolutionary history, contributions to plant phenotypic diversity, and role in adaptation. This review summarizes the main findings and progress of genome-wide identification and characterization studies of DOF TFs in Viridiplantae, exposing their roles as players in plant adaptation and a glimpse of their evolutionary history. We also present updated data on the identification and number of DOF genes in native and wild species. Altogether, these data, comprising a phylogenetic analysis of 2124 DOF homologs spanning 83 different species, will contribute to identifying new functional DOF groups, adding to our understanding of the mechanisms driving plant evolution and offering valuable insights into their potential applications.</p>","PeriodicalId":12557,"journal":{"name":"Genetics and Molecular Biology","volume":"46 3 Suppl 1","pages":"e20230109"},"PeriodicalIF":2.1,"publicationDate":"2024-02-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10842470/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139691631","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Transcriptional signature of host shift in the seed beetle Zabrotes subfasciatus. 种子甲虫 Zabrotes subfasciatus 宿主转移的转录特征。
IF 2.1 4区 生物学
Genetics and Molecular Biology Pub Date : 2024-02-05 eCollection Date: 2024-01-01 DOI: 10.1590/1678-4685-GMB-2023-0148
Pedro Augusto da Pos Rodrigues, Juliana Ramos Martins, Bianca Corrêa Capizzani, Lucas Takashi Araujo Hamasaki, Zilá Luz Paulino Simões, Isabel Ribeiro do Valle Teixeira, Angel Roberto Barchuk
{"title":"Transcriptional signature of host shift in the seed beetle Zabrotes subfasciatus.","authors":"Pedro Augusto da Pos Rodrigues, Juliana Ramos Martins, Bianca Corrêa Capizzani, Lucas Takashi Araujo Hamasaki, Zilá Luz Paulino Simões, Isabel Ribeiro do Valle Teixeira, Angel Roberto Barchuk","doi":"10.1590/1678-4685-GMB-2023-0148","DOIUrl":"10.1590/1678-4685-GMB-2023-0148","url":null,"abstract":"<p><p>In phytophagous insects, adaptation to a new host is a dynamic process, in which early and later steps may be underpinned by different features of the insect genome. Here, we tested the hypothesis that early steps of this process are underpinned by a shift in gene expression patterns. We set up a short-term artificial selection experiment (10 generations) for the use of an alternative host (Cicer arietinum) on populations of the bean beetle Zabrotes subfasciatus. Using Illumina sequencing on young adult females, we show the selected populations differ in the expression of genes associated to stimuli, signalling, and developmental processes. Particularly, the \"C. arietinum\" population shows upregulation of histone methylation genes, which may constitute a strategy for fine-tuning the insect global gene expression network. Using qPCR on body regions, we demonstrated that the \"Phaseolus vulgaris\" population upregulates the genes polygalacturonase and egalitarian and that the expression of an odorant receptor transcript variant changes over generations. Moreover, in this population we detected the existence of vitellogenin (Vg) variants in both males and females, possibly harbouring canonical reproductive function in females and extracellular unknown functions in males. This study provides the basis for future genomic investigations seeking to shed light on the nature of the proximate mechanisms involved in promoting differential gene expression associated to insect development and adaptation to new hosts.</p>","PeriodicalId":12557,"journal":{"name":"Genetics and Molecular Biology","volume":"47 1","pages":"e20230148"},"PeriodicalIF":2.1,"publicationDate":"2024-02-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10851049/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139691634","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Erratum: Neonatal screening for spinal muscular atrophy: A pilot study in Brazil. 勘误:新生儿脊髓性肌萎缩症筛查:巴西试点研究。
IF 2.1 4区 生物学
Genetics and Molecular Biology Pub Date : 2024-02-02 DOI: 10.1590/1678-4685-GMB-2023-0126er
{"title":"Erratum: Neonatal screening for spinal muscular atrophy: A pilot study in Brazil.","authors":"","doi":"10.1590/1678-4685-GMB-2023-0126er","DOIUrl":"10.1590/1678-4685-GMB-2023-0126er","url":null,"abstract":"<p><p>[This corrects the article doi: ].</p>","PeriodicalId":12557,"journal":{"name":"Genetics and Molecular Biology","volume":"46 3 Suppl 1","pages":"e20230126er"},"PeriodicalIF":2.1,"publicationDate":"2024-02-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10905211/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139971582","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Structure-based prediction of protein-protein interaction network in rice. 基于结构的水稻蛋白质相互作用网络预测
IF 2.1 4区 生物学
Genetics and Molecular Biology Pub Date : 2024-02-02 eCollection Date: 2024-01-01 DOI: 10.1590/1678-4685-GMB-2023-0068
Fangnan Sun, Yaxin Deng, Xiaosong Ma, Yuan Liu, Lingxia Zhao, Shunwu Yu, Lida Zhang
{"title":"Structure-based prediction of protein-protein interaction network in rice.","authors":"Fangnan Sun, Yaxin Deng, Xiaosong Ma, Yuan Liu, Lingxia Zhao, Shunwu Yu, Lida Zhang","doi":"10.1590/1678-4685-GMB-2023-0068","DOIUrl":"10.1590/1678-4685-GMB-2023-0068","url":null,"abstract":"<p><p>Comprehensive protein-protein interaction (PPI) maps are critical for understanding the functional organization of the proteome, but challenging to produce experimentally. Here, we developed a computational method for predicting PPIs based on protein docking. Evaluation of performance on benchmark sets demonstrated the ability of the docking-based method to accurately identify PPIs using predicted protein structures. By employing the docking-based method, we constructed a structurally resolved PPI network consisting of 24,653 interactions between 2,131 proteins, which greatly extends the current knowledge on the rice protein-protein interactome. Moreover, we mapped the trait-associated single nucleotide polymorphisms (SNPs) to the structural interactome, and computationally identified 14 SNPs that had significant consequences on PPI network. The protein structural interactome map provided a resource to facilitate functional investigation of PPI-perturbing alleles associated with agronomically important traits in rice.</p>","PeriodicalId":12557,"journal":{"name":"Genetics and Molecular Biology","volume":"47 1","pages":"e20230068"},"PeriodicalIF":2.1,"publicationDate":"2024-02-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10849033/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139691633","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Brazilian women in Bioinformatics: Challenges and opportunities. 生物信息学领域的巴西妇女:挑战与机遇。
IF 1.7 4区 生物学
Genetics and Molecular Biology Pub Date : 2024-01-22 eCollection Date: 2024-01-01 DOI: 10.1590/1678-4685-GMB-2023-0134
Thayne Woycinck Kowalski, Giovanna Câmara Giudicelli, Maria Clara de Freitas Pinho, Marília Körbes Rockenbach, Miriãn Ferrão Maciel-Fiuza, Mariana Recamonde-Mendoza, Fernanda Sales Luiz Vianna
{"title":"Brazilian women in Bioinformatics: Challenges and opportunities.","authors":"Thayne Woycinck Kowalski, Giovanna Câmara Giudicelli, Maria Clara de Freitas Pinho, Marília Körbes Rockenbach, Miriãn Ferrão Maciel-Fiuza, Mariana Recamonde-Mendoza, Fernanda Sales Luiz Vianna","doi":"10.1590/1678-4685-GMB-2023-0134","DOIUrl":"10.1590/1678-4685-GMB-2023-0134","url":null,"abstract":"<p><p>Bioinformatics is a growing research field that received great notoriety in the years of the COVID-19 pandemic. It is a very integrative area, comprising professionals from science, technology, engineering, and mathematics (STEM). In agreement with the other STEM areas, several women have greatly contributed to bioinformatics ascension; however, they had to surpass prejudice and stereotypes to achieve recognition and leadership positions, a path that studies have demonstrated to be more comfortable to their male colleagues. In this review, we discuss the several difficulties that women in STEM, including bioinformatics, surpass during their careers. First, we present a historical context on bioinformatics and the main applications for this area. Then, we discuss gender disparity in STEM and present the challenges that still contribute to women's inequality in STEM compared to their male colleagues. We also present the opportunities and the transformation that we can start, acting in academia, inside the family and school environments, and as a society, hence contributing to gender equality in STEM. Finally, we discuss specific challenges in the bioinformatics field and how we can act to overcome them, especially in low and middle-income countries, such as Brazil.</p>","PeriodicalId":12557,"journal":{"name":"Genetics and Molecular Biology","volume":"46 3 Suppl 1","pages":"e20230134"},"PeriodicalIF":1.7,"publicationDate":"2024-01-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10829893/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139520511","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Oral microbiota, co-evolution, and implications for health and disease: The case of indigenous peoples. 口腔微生物群、共同进化以及对健康和疾病的影响:原住民的案例。
IF 1.7 4区 生物学
Genetics and Molecular Biology Pub Date : 2024-01-22 eCollection Date: 2024-01-01 DOI: 10.1590/1678-4685-GMB-2023-0129
Mariana Marcano-Ruiz, Thaynara Lima, Gustavo Medina Tavares, Maria Thereza Schmitt Mesquita, Luana da Silva Kaingang, Lavínia Schüler-Faccini, Maria Cátira Bortolini
{"title":"Oral microbiota, co-evolution, and implications for health and disease: The case of indigenous peoples.","authors":"Mariana Marcano-Ruiz, Thaynara Lima, Gustavo Medina Tavares, Maria Thereza Schmitt Mesquita, Luana da Silva Kaingang, Lavínia Schüler-Faccini, Maria Cátira Bortolini","doi":"10.1590/1678-4685-GMB-2023-0129","DOIUrl":"10.1590/1678-4685-GMB-2023-0129","url":null,"abstract":"<p><p>Evidence indicates that oral microbiota plays a crucial role in human health and disease. For instance, diseases with multifactorial etiology, such as periodontitis and caries, which cause a detrimental impact on human well-being and health, can be caused by alterations in the host-microbiota interactions, where non-pathogenic bacteria give way to pathogenic orange/red-complex bacterial species (a change from a eubiotic to dysbiotic state). In this scenario, where thousands of oral microorganisms, including fungi, archaea, and phage species, and their host are co-evolving, a set of phenomena, such as the arms race and Red or Black Queen dynamics, are expected to operate. We review concepts on the subject and revisit the nature of bacterial complexes linked to oral health and diseases, as well as the problem of the bacterial resistome in the face of the use of antibiotics and what is the impact of this on the evolutionary trajectory of the members of this symbiotic ecosystem. We constructed a 16SrRNA tree to show that adaptive consortia of oral bacterial complexes do not necessarily rescue phylogenetic relationships. Finally, we remember that oral health is not exempt from health disparity trends in some populations, such as Native Americans, when compared with non-Indigenous people.</p>","PeriodicalId":12557,"journal":{"name":"Genetics and Molecular Biology","volume":"46 3 Suppl 1","pages":"e20230129"},"PeriodicalIF":1.7,"publicationDate":"2024-01-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10829892/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139520517","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Broken silence: 22,841 predicted deleterious synonymous variants identified in the human exome through computational analysis. 打破沉默:通过计算分析在人类外显子组中发现 22,841 个预测的有害同义变异。
IF 1.7 4区 生物学
Genetics and Molecular Biology Pub Date : 2024-01-22 eCollection Date: 2024-01-01 DOI: 10.1590/1678-4685-GMB-2023-0125
Ana Carolina Mello, Delva Leao, Luis Dias, Felipe Colombelli, Mariana Recamonde-Mendoza, Andreia Carina Turchetto-Zolet, Ursula Matte
{"title":"Broken silence: 22,841 predicted deleterious synonymous variants identified in the human exome through computational analysis.","authors":"Ana Carolina Mello, Delva Leao, Luis Dias, Felipe Colombelli, Mariana Recamonde-Mendoza, Andreia Carina Turchetto-Zolet, Ursula Matte","doi":"10.1590/1678-4685-GMB-2023-0125","DOIUrl":"10.1590/1678-4685-GMB-2023-0125","url":null,"abstract":"<p><p>Synonymous single nucleotide variants (sSNVs) do not alter the primary structure of a protein, thus it was previously accepted that they were neutral. Recently, several studies demonstrated their significance to a range of diseases. Still, variant prioritization strategies lack focus on sSNVs. Here, we identified 22,841 deleterious synonymous variants in 125,748 human exomes using two in silico predictors (SilVA and CADD). While 98.2% of synonymous variants are classified as neutral, 1.8% are predicted to be deleterious, yielding an average of 9.82 neutral and 0.18 deleterious sSNVs per exome. Further investigation of prediction features via Heterogeneous Ensemble Feature Selection revealed that impact on amino acid sequence and conservation carry the most weight for a deleterious prediction. Thirty nine detrimental sSNVs are not rare and are located on disease associated genes. Ten distinct putatively non-deleterious sSNVs are likely to be under positive selection in the North-Western European and East Asian populations. Taken together our analysis gives voice to the so-called silent mutations as we propose a robust framework for evaluating the deleteriousness of sSNVs in variant prioritization studies.</p>","PeriodicalId":12557,"journal":{"name":"Genetics and Molecular Biology","volume":"46 3 Suppl 1","pages":"e20230125"},"PeriodicalIF":1.7,"publicationDate":"2024-01-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10804382/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139520515","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Tailed bacteriophages (Caudoviricetes) dominate the microbiome of a diseased stingless bee. 尾部噬菌体(Caudoviricetes)在患病无刺蜂的微生物组中占主导地位。
IF 1.7 4区 生物学
Genetics and Molecular Biology Pub Date : 2024-01-19 eCollection Date: 2024-01-01 DOI: 10.1590/1678-4685-GMB-2023-0120
Lilian Caesar, Karen Luisa Haag
{"title":"Tailed bacteriophages (Caudoviricetes) dominate the microbiome of a diseased stingless bee.","authors":"Lilian Caesar, Karen Luisa Haag","doi":"10.1590/1678-4685-GMB-2023-0120","DOIUrl":"10.1590/1678-4685-GMB-2023-0120","url":null,"abstract":"<p><p>Bacteriophages, viruses that infect bacterial hosts, are known to rule the dynamics and diversity of bacterial populations in a number of ecosystems. Bacterial communities residing in the gut of animals, known as the gut microbiome, have revolutionized our understanding of many diseases. However, the gut phageome, while of apparent importance in this context, remains an underexplored area of research. Here we identify for the first time genomic sequences from tailed viruses (Caudoviricetes) that are associated with the microbiome of stingless bees (Melipona quadrifasciata). Both DNA and RNA were extracted from virus particles isolated from healthy and diseased forager bees, the latter showing symptoms from an annual syndrome that only affects M. quadrifasciata. Viral contigs from previously sequenced metagenomes of healthy and diseased forager bees were used for the analyses. Using conserved proteins deduced from their genomes, we found that Caudoviricetes were only present in the worker bee gut microbiome from diseased stingless bees. The most abundant phages are phylogenetically related to phages that infect Gram-positive bacteria from the order Lactobacillales and Gram-negative bacteria from the genus Gilliamella and Bartonella, that are common honey bee symbionts. The potential implication of these viruses in the M. quadrifasciata syndrome is discussed.</p>","PeriodicalId":12557,"journal":{"name":"Genetics and Molecular Biology","volume":"46 3 Suppl 1","pages":"e20230120"},"PeriodicalIF":1.7,"publicationDate":"2024-01-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10802228/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139512370","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Position Weight Matrix or Acyclic Probabilistic Finite Automaton: Which model to use? A decision rule inferred for the prediction of transcription factor binding sites. 位置权重矩阵或循环概率有限自动机:使用哪种模型?用于预测转录因子结合位点的决策规则推论。
IF 2.1 4区 生物学
Genetics and Molecular Biology Pub Date : 2024-01-19 eCollection Date: 2024-01-01 DOI: 10.1590/1678-4685-GMB-2023-0048
Guilherme Miura Lavezzo, Marcelo de Souza Lauretto, Luiz Paulo Moura Andrioli, Ariane Machado-Lima
{"title":"Position Weight Matrix or Acyclic Probabilistic Finite Automaton: Which model to use? A decision rule inferred for the prediction of transcription factor binding sites.","authors":"Guilherme Miura Lavezzo, Marcelo de Souza Lauretto, Luiz Paulo Moura Andrioli, Ariane Machado-Lima","doi":"10.1590/1678-4685-GMB-2023-0048","DOIUrl":"10.1590/1678-4685-GMB-2023-0048","url":null,"abstract":"<p><p>Prediction of transcription factor binding sites (TFBS) is an example of application of Bioinformatics where DNA molecules are represented as sequences of A, C, G and T symbols. The most used model in this problem is Position Weight Matrix (PWM). Notwithstanding the advantage of being simple, PWMs cannot capture dependency between nucleotide positions, which may affect prediction performance. Acyclic Probabilistic Finite Automata (APFA) is an alternative model able to accommodate position dependencies. However, APFA is a more complex model, which means more parameters have to be learned. In this paper, we propose an innovative method to identify when position dependencies influence preference for PWMs or APFAs. This implied using position dependency features extracted from 1106 sets of TFBS to infer a decision tree able to predict which is the best model - PWM or APFA - for a given set of TFBSs. According to our results, as few as three pinpointed features are able to choose the best model, providing a balance of performance (average precision) and model simplicity.</p>","PeriodicalId":12557,"journal":{"name":"Genetics and Molecular Biology","volume":"46 4","pages":"e20230048"},"PeriodicalIF":2.1,"publicationDate":"2024-01-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10945726/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139570329","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
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