Matching Techniques in Genomic Sequences for Motif Searching

2009 ◽  
pp. 319-330
Author(s):  
K. R. Venugopal ◽  
K. G. Srinivasa ◽  
L. M. Patnaik
Keyword(s):  
Genomic Sequences ◽  
Motif Searching ◽  
Matching Techniques

Survey of transposable elements from rice genomic sequences

2001 ◽  
Vol 25 (2) ◽  
pp. 169-179 ◽  
Author(s):  
Kime Turcotte ◽  
Sujatha Srinivasan ◽  
Thomas Bureau
Keyword(s):  
Transposable Elements ◽  
Genomic Sequences

scholarly journals Analysis of HLA-G long-read genomic sequences in mother–offspring pairs with preeclampsia

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Ayako Nishizawa ◽  
Kazuki Kumada ◽  
Keiko Tateno ◽  
Maiko Wagata ◽  
Sakae Saito ◽  
...  
Keyword(s):  
Single Molecule ◽  
Gene Polymorphisms ◽  
Genomic Dna ◽  
Genomic Sequences ◽  
Genomic Sequencing ◽  
Public Database ◽  
Coding Sequences ◽  
Pacbio Rs Ii ◽  
Potential Association ◽  
Long Read

AbstractPreeclampsia is a pregnancy-induced disorder that is characterized by hypertension and is a leading cause of perinatal and maternal–fetal morbidity and mortality. HLA-G is thought to play important roles in maternal–fetal immune tolerance, and the associations between HLA-G gene polymorphisms and the onset of pregnancy-related diseases have been explored extensively. Because contiguous genomic sequencing is difficult, the association between the HLA-G genotype and preeclampsia onset is controversial. In this study, genomic sequences of the HLA-G region (5.2 kb) from 31 pairs of mother–offspring genomic DNA samples (18 pairs from normal pregnancies/births and 13 from preeclampsia births) were obtained by single-molecule real-time sequencing using the PacBio RS II platform. The HLA-G alleles identified in our cohort matched seven known HLA-G alleles, but we also identified two new HLA-G alleles at the fourth-field resolution and compared them with nucleotide sequences from a public database that consisted of coding sequences that cover the 3.1-kb HLA-G gene span. Intriguingly, a potential association between preeclampsia onset and the poly T stretch within the downstream region of the HLA-G*01:01:01:01 allele was found. Our study suggests that long-read sequencing of HLA-G will provide clues for characterizing HLA-G variants that are involved in the pathophysiology of preeclampsia.

scholarly journals Dissecting the chromosome-level genome of the Asian Clam (Corbicula fluminea)

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Tongqing Zhang ◽  
Jiawen Yin ◽  
Shengkai Tang ◽  
Daming Li ◽  
Xiankun Gu ◽  
...  
Keyword(s):  
De Novo ◽  
Corbicula Fluminea ◽  
Gene Families ◽  
Ruditapes Philippinarum ◽  
Genomic Sequences ◽  
Future Research ◽  
Asian Clam ◽  
Sequencing Technologies ◽  
East And Southeast Asia ◽  
Clam Corbicula

AbstractThe Asian Clam (Corbicula fluminea) is a valuable commercial and medicinal bivalve, which is widely distributed in East and Southeast Asia. As a natural nutrient source, the clam is rich in protein, amino acids, and microelements. The genome of C. fluminea has not yet been characterized; therefore, genome-assisted breeding and improvements cannot yet be implemented. In this work, we present a de novo chromosome-scale genome assembly of C. fluminea using PacBio and Hi-C sequencing technologies. The assembled genome comprised 4728 contigs, with a contig N50 of 521.06 Kb, and 1,215 scaffolds with a scaffold N50 of 70.62 Mb. More than 1.51 Gb (99.17%) of genomic sequences were anchored to 18 chromosomes, of which 1.40 Gb (92.81%) of genomic sequences were ordered and oriented. The genome contains 38,841 coding genes, 32,591 (83.91%) of which were annotated in at least one functional database. Compared with related species, C. fluminea had 851 expanded gene families and 191 contracted gene families. The phylogenetic tree showed that C. fluminea diverged from Ruditapes philippinarum, ~ 228.89 million years ago (Mya), and the genomes of C. fluminea and R. philippinarum shared 244 syntenic blocks. Additionally, we identified 2 MITF members and 99 NLRP members in C. fluminea genome. The high-quality and chromosomal Asian Clam genome will be a valuable resource for a range of development and breeding studies of C. fluminea in future research.

scholarly journals Text Classification in Clinical Practice Guidelines Using Machine-Learning Assisted Pattern-Based Approach

2021 ◽  
Vol 11 (8) ◽  
pp. 3296
Author(s):  
Musarrat Hussain ◽  
Jamil Hussain ◽  
Taqdir Ali ◽  
Syed Imran Ali ◽  
Hafiz Syed Muhammad Bilal ◽  
...  
Keyword(s):  
Machine Learning ◽  
Decision Making ◽  
Clinical Practice ◽  
Clinical Practice Guidelines ◽  
Practice Guidelines ◽  
Machine Learning Algorithms ◽  
Nominal Group ◽  
Specific Information ◽  
Matching Techniques ◽  
Disease Specific

Clinical Practice Guidelines (CPGs) aim to optimize patient care by assisting physicians during the decision-making process. However, guideline adherence is highly affected by its unstructured format and aggregation of background information with disease-specific information. The objective of our study is to extract disease-specific information from CPG for enhancing its adherence ratio. In this research, we propose a semi-automatic mechanism for extracting disease-specific information from CPGs using pattern-matching techniques. We apply supervised and unsupervised machine-learning algorithms on CPG to extract a list of salient terms contributing to distinguishing recommendation sentences (RS) from non-recommendation sentences (NRS). Simultaneously, a group of experts also analyzes the same CPG and extract the initial patterns “Heuristic Patterns” using a group decision-making method, nominal group technique (NGT). We provide the list of salient terms to the experts and ask them to refine their extracted patterns. The experts refine patterns considering the provided salient terms. The extracted heuristic patterns depend on specific terms and suffer from the specialization problem due to synonymy and polysemy. Therefore, we generalize the heuristic patterns to part-of-speech (POS) patterns and unified medical language system (UMLS) patterns, which make the proposed method generalize for all types of CPGs. We evaluated the initial extracted patterns on asthma, rhinosinusitis, and hypertension guidelines with the accuracy of 76.92%, 84.63%, and 89.16%, respectively. The accuracy increased to 78.89%, 85.32%, and 92.07% with refined machine-learning assistive patterns, respectively. Our system assists physicians by locating disease-specific information in the CPGs, which enhances the physicians’ performance and reduces CPG processing time. Additionally, it is beneficial in CPGs content annotation.

scholarly journals The fermionic universal one-loop effective action

2020 ◽  
Vol 2020 (11) ◽  
Author(s):  
Sebastian A. R. Ellis ◽  
Jérémie Quevillon ◽  
Pham Ngoc Hoa Vuong ◽  
Tevong You ◽  
Zhengkang Zhang
Keyword(s):  
Path Integral ◽  
Effective Action ◽  
Covariant Derivative ◽  
Heavy Fermion ◽  
Axial Vector ◽  
Derivative Expansion ◽  
Universal Structure ◽  
Pseudo Scalar ◽  
Matching Techniques ◽  
Analytical Expressions

Abstract Recent development of path integral matching techniques based on the covariant derivative expansion has made manifest a universal structure of one-loop effective Lagrangians. The universal terms can be computed once and for all to serve as a reference for one-loop matching calculations and to ease their automation. Here we present the fermionic universal one-loop effective action (UOLEA), resulting from integrating out heavy fermions (Dirac or Majorana) with scalar, pseudo-scalar, vector and axial-vector couplings. We also clarify the relation of the new terms computed here to terms previously computed in the literature and those that remain to complete the UOLEA. Our results can be readily used to efficiently obtain analytical expressions for effective operators arising from heavy fermion loops [13].

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