scholarly journals BARKODING DNA BURUNG ELANG (FAMILI ACCIPITRIDAE) DI INDONESIA

2018 ◽  
Vol 17 (2) ◽  
Author(s):  
Moch Syamsul Arifin Zein
Keyword(s):  
Animal Species ◽  
Distance Matrix ◽  
Pairwise Distance ◽  
Coi Gene ◽  
Local Alignment ◽  
Protein Coding ◽  
Genetic Distance Matrix ◽  
The Family ◽  
Search Tool ◽  
Identification Tool

The cytochrome c oxidase subunit I (COI) gene is a reprensentative of all the protein-coding genes of the mitochondrial DNA genome that has been widely used as an animal species identification tool. In this study, 86 sequences of DNA barcodes of members of the family Accipitridae in Indonesia including Nisaetus bartelsi, Nisaetus cirrhatus, Haliaeetus leucogaster, Spilornis cheela, Haliastur indus, and 11 sequences from Genbank were examined. Each species was confirmed through the Basic Local Alignment Search Tool (BLAST). The construction of phylogeny trees based on COI gene sequences was performed by the Neighbors-joining method where the calculation of the genetic distance matrix with the Kimura 2-parameter model was implemented in pairwise distance calculation in the Mega version 6.05 programe. The results of the analysis showed that the divergence within species ranged from 0 to 0.3% (0.13 ± 0.12%), between species ranged from 1.6 to 18.5% (12.8 ± 3.73%), between genera ranged from 13 to 18.6%, and the average in the Accipitridae Family was 11.8%. Therefore, it could form clusters in each species cohesively and clearly separated between the taxa analyzed.

scholarly journals Fish Identification based on Partial Fragments of The Mitochondrial COI Subunit I Gene

2021 ◽  
Vol 322 ◽  
pp. 01038
Author(s):  
Tuah N. M. Wulandari
Keyword(s):  
Phylogenetic Tree ◽  
Coi Gene ◽  
Local Alignment ◽  
Mtdna Sequences ◽  
Mitochondrial Coi ◽  
Search Tool ◽  
Very High ◽  
I Gene

The mtDNA sequences revealed that several of the fish studied were Hampala macrolepidota and Barbonymus gonionotus. The objective of this research was to learn the pattern of COI gene in mtDNA and establish a phylogenetic tree. Basic Local Alignment Search Tool-nucleotide (BLASTn) confirmed that Barbonymus gonionotus froma the Ranau Lake, South Sumatera has 100% matching ranges to the species from Memberamo River (Indonesia), India, Bangladesh, Thailand (Mae Khlong), Indo-Myanmar, and Malaysia_1. The lowest closeness (98.76%) is related to species from Thailand (Lower Ing). The Blast investigation appears us that the level of familiarity was very high, it is coming to 98-100% in Barbonymus gonionotus. Hampala macrolepidota had 100% matching ranges to the species from Indonesia (SouthaSumatera_1) and Vietnam. They had 99.05%-99.84% closeness from Malaysia_1,2&3, Indonesia (South Sumatera_2&3, Java and Bali_1,2&3).

scholarly journals Molecular classification and comparative phylogeographic study of insectivorous bat species (Pipisitrellus coromandra) from Punjab, Pakistan

2022 ◽  
Vol 82 ◽  
Author(s):  
Z. Ahmad ◽  
M. H. Abbasi ◽  
S. R. Ahmad ◽  
N. Sheikh
Keyword(s):  
Molecular Classification ◽  
Genetic Distances ◽  
Coi Gene ◽  
Local Alignment ◽  
Identity Match ◽  
Gene Coi ◽  
Search Tool ◽  
Identity Score ◽  
First Time

Abstract Molecular based identification of bat fauna in Pakistan has been relatively less explored. The current study was therefore planned to report for the first time the molecular classification of insectivorous bats (Pipistrellus coromandra) based on mitochondrion gene (COI) from Punjab, Pakistan. Specimens were collected from five different locations followed by DNA extraction with subsequent gene amplification and sequencing. All samples in the study had shown close identity matches with species (Pipistrellus coromandra) from India and (Pipistrellus tenuis) from Vietnam with percentage identity score of 96.11 and 95.58 respectively except one sequence which only revealed 86.78% identity match on Basic Local Alignment Search Tool (BLAST) and could only be assigned to genus level Pipistrellus sp. The results indicated negligible intra-population genetic distance among collected samples whereas the comparison with species from other countries had shown high intraspecific (P. coromandra) and interspecific (P. tenuis) mean genetic distances. The current study hence successfully proved the efficiency of COI gene as a molecular marker for species identification and in analyzing the patterns of genetic variation with species from other countries.

scholarly journals Phylogenetic of Marble Goby (Oxyeleotris marmorata Blkr.) in South Sumatra Based on Cytochrome C Oxidase Subunit I (COI) Gene

10.4194/ga433 ◽  
2021 ◽  
Vol 6 (1) ◽  
Author(s):  
Mochamad Syaifudin ◽  
Dade Jubaedah ◽  
Ferdinand Hukama Taqwa ◽  
Ria Octaviani
Keyword(s):  
Genetic Distance ◽  
Coi Gene ◽  
Local Alignment ◽  
Coi Mtdna ◽  
Oxidase Subunit ◽  
Three Samples ◽  
Search Tool ◽  
Pcr Method ◽  
Polymerase Chain ◽  
Musi River

Marble goby (Oxyeleotris marmorata) in Indonesia, spread across Sumatra, Kalimantan and Papua. The purpose of this study was to utilize a sequence of mitochondrial DNA Cytochrome Oxidase Subunit I gene, to analyze the phylogenetic tree and genetic distance between cultured and captured populations. This research was conducted on March-August 2020. The methods used in barcoding species were DNA isolation, amplification using PCR (Polymerase Chain Reaction) and sequencing of the COI mtDNA gene. The domesticated samples (n=3) were collected from Gandus Fish Seed Center (GFSC), while the wild samples (n=3) were captured from the Musi River in Beruge Village, Babat Toman District, both in Musi Banyuasin Regency. The sequenced COI mtDNA gene fragments were obtained from the PCR method. Three samples performed good PCR results, while the other three didn’t amplify properly. After the editing process, the COI gene sequencing produced a nucleotide length of 610 bp. Based on the BLAST (Basic Local Alignment Search Tool), domesticated marble goby (OMD2, OMD3) was in the same cluster with marble goby from the Musi River (OMS3). The genetic distance indicated that two specimens of domesticated marble goby were 100% identical, while the wild (OMS3) indicated a genetic distance of 0.0066 to domesticated species.

The Influence of Memory-Aware Computation on Distributed BLAST

2019 ◽  
Vol 14 (2) ◽  
pp. 157-163
Author(s):  
Majid Hajibaba ◽  
Mohsen Sharifi ◽  
Saeid Gorgin
Keyword(s):  
Search Time ◽  
Genomic Research ◽  
Local Alignment ◽  
Negative Effects ◽  
Sequencing Technologies ◽  
Percent Improvement ◽  
Fast Processing ◽  
Search Tool ◽  
Memory Awareness ◽  
Generation Sequencing

Background: One of the pivotal challenges in nowadays genomic research domain is the fast processing of voluminous data such as the ones engendered by high-throughput Next-Generation Sequencing technologies. On the other hand, BLAST (Basic Local Alignment Search Tool), a longestablished and renowned tool in Bioinformatics, has shown to be incredibly slow in this regard. Objective: To improve the performance of BLAST in the processing of voluminous data, we have applied a novel memory-aware technique to BLAST for faster parallel processing of voluminous data. Method: We have used a master-worker model for the processing of voluminous data alongside a memory-aware technique in which the master partitions the whole data in equal chunks, one chunk for each worker, and consequently each worker further splits and formats its allocated data chunk according to the size of its memory. Each worker searches every split data one-by-one through a list of queries. Results: We have chosen a list of queries with different lengths to run insensitive searches in a huge database called UniProtKB/TrEMBL. Our experiments show 20 percent improvement in performance when workers used our proposed memory-aware technique compared to when they were not memory aware. Comparatively, experiments show even higher performance improvement, approximately 50 percent, when we applied our memory-aware technique to mpiBLAST. Conclusion: We have shown that memory-awareness in formatting bulky database, when running BLAST, can improve performance significantly, while preventing unexpected crashes in low-memory environments. Even though distributed computing attempts to mitigate search time by partitioning and distributing database portions, our memory-aware technique alleviates negative effects of page-faults on performance.

scholarly journals Sequencing of Organellar Genomes of Nowellia curvifolia (Cephaloziaceae Jungermanniales) Revealed the Smallest Plastome with Complete Gene Set and High Intraspecific Variation Suggesting Cryptic Speciation

Diversity ◽  
2021 ◽  
Vol 13 (2) ◽  
pp. 81
Author(s):  
Jakub Sawicki ◽  
Katarzyna Krawczyk ◽  
Monika Ślipiko ◽  
Monika Szczecińska
Keyword(s):  
Cryptic Speciation ◽  
Editing Event ◽  
Protein Coding ◽  
Gene Set ◽  
Protein Coding Genes ◽  
Organellar Genomes ◽  
The Family ◽  
Leafy Liverwort ◽  
Aneura Mirabilis ◽  
First Time

The leafy liverwort Nowellia curvifolia is a widespread Holarctic species belonging to the family Cephaloziaceae. It is made up of a newly sequenced, assembled and annotated organellar genomes of two European specimens, which revealed the structure typical for liverworts, but also provided new insights into its microevolution. The plastome of N. curvifolia is the second smallest among photosynthetic liverworts, with the shortest known inverted repeats. Moreover, it is the smallest liverwort genome with a complete gene set, since two smaller genomes of Aneura mirabilis and Cololejeunea lanciloba are missing six and four protein-coding genes respectively. The reduction of plastome size in leafy liverworts seems to be mainly impacted by deletion within specific region between psbA and psbD genes. The comparative intraspecific analysis revealed single SNPs difference among European individuals and a low number of 35 mutations differentiating European and North American specimens. However, the genetic resources of Asian specimen enabled to identify 1335 SNPs in plastic protein-coding genes suggesting an advanced cryptic speciation within N. curvifolia or the presence of undescribed morphospecies in Asia. Newly sequenced mitogenomes from European specimens revealed identical gene content and structure to previously published and low intercontinental differentiation limited to one substitution and three indels. The RNA-seq based RNA editing analysis revealed 17 and 127 edited sites in plastome and mitogenome respectively including one non-canonical editing event in plastid chiL gene. The U to C editing is common in non-seed plants, but in liverwort plastome is reported for the first time.

scholarly journals Chatbot to improve learning punctuation in Spanish and to enhance open and flexible learning environments

2021 ◽  
Vol 18 (1) ◽  
Author(s):  
Esteban Vázquez-Cano ◽  
Santiago Mengual-Andrés ◽  
Eloy López-Meneses
Keyword(s):  
Learning Process ◽  
Latent Dirichlet Allocation ◽  
Distance Matrix ◽  
Ease Of Use ◽  
Three Dimensions ◽  
Pairwise Distance ◽  
Control Group ◽  
Quantitative Methodology ◽  
Quasi Experimental ◽  
Experimental Group

AbstractThe objective of this article is to analyze the didactic functionality of a chatbot to improve the results of the students of the National University of Distance Education (UNED / Spain) in accessing the university in the subject of Spanish Language. For this, a quasi-experimental experiment was designed, and a quantitative methodology was used through pretest and posttest in a control and experimental group in which the effectiveness of two teaching models was compared, one more traditional based on exercises written on paper and another based on interaction with a chatbot. Subsequently, the perception of the experimental group in an academic forum about the educational use of the chatbot was analyzed through text mining with tests of Latent Dirichlet Allocation (LDA), pairwise distance matrix and bigrams. The quantitative results showed that the students in the experimental group substantially improved the results compared to the students with a more traditional methodology (experimental group / mean: 32.1346 / control group / mean: 28.4706). Punctuation correctness has been improved mainly in the usage of comma, colon and periods in different syntactic patterns. Furthermore, the perception of the students in the experimental group showed that they positively value chatbots in their teaching–learning process in three dimensions: greater “support” and companionship in the learning process, as they perceive greater interactivity due to their conversational nature; greater “feedback” and interaction compared to the more traditional methodology and, lastly, they especially value the ease of use and the possibility of interacting and learning anywhere and anytime.

scholarly journals Predicting bacteriophage hosts based on sequences of annotated receptor-binding proteins

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Dimitri Boeckaerts ◽  
Michiel Stock ◽  
Bjorn Criel ◽  
Hans Gerstmans ◽  
Bernard De Baets ◽  
...  
Keyword(s):  
Machine Learning ◽  
Predictive Model ◽  
Receptor Binding ◽  
Bacterial Infections ◽  
Sequence Data ◽  
Sequence Similarity ◽  
Area Under The Curve ◽  
Local Alignment ◽  
Search Tool ◽  
Different Levels

AbstractNowadays, bacteriophages are increasingly considered as an alternative treatment for a variety of bacterial infections in cases where classical antibiotics have become ineffective. However, characterizing the host specificity of phages remains a labor- and time-intensive process. In order to alleviate this burden, we have developed a new machine-learning-based pipeline to predict bacteriophage hosts based on annotated receptor-binding protein (RBP) sequence data. We focus on predicting bacterial hosts from the ESKAPE group, Escherichia coli, Salmonella enterica and Clostridium difficile. We compare the performance of our predictive model with that of the widely used Basic Local Alignment Search Tool (BLAST). Our best-performing predictive model reaches Precision-Recall Area Under the Curve (PR-AUC) scores between 73.6 and 93.8% for different levels of sequence similarity in the collected data. Our model reaches a performance comparable to that of BLASTp when sequence similarity in the data is high and starts outperforming BLASTp when sequence similarity drops below 75%. Therefore, our machine learning methods can be especially useful in settings in which sequence similarity to other known sequences is low. Predicting the hosts of novel metagenomic RBP sequences could extend our toolbox to tune the host spectrum of phages or phage tail-like bacteriocins by swapping RBPs.

scholarly journals Kelch 13-propeller polymorphisms in Plasmodium falciparum from Jazan region, southwest Saudi Arabia

2020 ◽  
Vol 19 (1) ◽  
Author(s):  
Ommer Mohammed Dafalla ◽  
Mohammed Alzahrani ◽  
Ahmed Sahli ◽  
Mohammed Abdulla Al Helal ◽  
Mohammad Mohammad Alhazmi ◽  
...  
Keyword(s):  
Plasmodium Falciparum ◽  
Saudi Arabia ◽  
Parasite Clearance ◽  
Sub Saharan Africa ◽  
Local Alignment ◽  
Nucleotide Polymorphisms ◽  
Gene Encoding ◽  
Synonymous Mutations ◽  
Search Tool ◽  
Sub Saharan

Abstract Background Artemisinin-based combination therapy (ACT) is recommended at the initial phase for treatment of Plasmodium falciparum, to reduce morbidity and mortality in all countries where malaria is endemic. Polymorphism in portions of P. falciparum gene encoding kelch (K13)-propeller domains is associated with delayed parasite clearance after ACT. Of about 124 different non-synonymous mutations, 46 have been identified in Southeast Asia (SEA), 62 in sub-Saharan Africa (SSA) and 16 in both the regions. This is the first study designed to analyse the prevalence of polymorphism in the P. falciparum k13-propeller domain in the Jazan region of southwest Saudi Arabia, where malaria is endemic. Methods One-hundred and forty P. falciparum samples were collected from Jazan region of southwest Saudi Arabia at three different times: 20 samples in 2011, 40 samples in 2016 and 80 samples in 2020 after the implementation of ACT. Plasmodium falciparum kelch13 (k13) gene DNA was extracted, amplified, sequenced, and analysed using a basic local alignment search tool (BLAST). Results This study obtained 51 non-synonymous (NS) mutations in three time groups, divided as follows: 6 single nucleotide polymorphisms (SNPs) ‘11.8%’ in samples collected in 2011 only, 3 (5.9%) in 2011and 2016, 5 (9.8%) in 2011 and 2020, 5 (9.8%) in 2016 only, 8 (15.7%) in 2016 and 2020, 14 (27.5%) in 2020 and 10 (19.6%) in all the groups. The BLAST revealed that the 2011 isolates were genetically closer to African isolates (53.3%) than Asian ones (46.7%). Interestingly, this proportion changed completely in 2020, to become closer to Asian isolates (81.6%) than to African ones (18.4%). Conclusions Despite the diversity of the identified mutations in the k13-propeller gene, these data did not report widespread artemisinin-resistant polymorphisms in the Jazan region where these samples were collected. Such a process would be expected to increase frequencies of mutations associated with the resistance of ACT.

scholarly journals Genetic Structure of Field Populations of Begomoviruses and of Their Vector Bemisia tabaci in Pakistan

2003 ◽  
Vol 93 (11) ◽  
pp. 1422-1429 ◽  
Author(s):  
Belén Simón ◽  
José Luis Cenis ◽  
Francisco Beitia ◽  
Saif Khalid ◽  
Ignacio M. Moreno ◽  
...  
Keyword(s):  
Genetic Structure ◽  
Bemisia Tabaci ◽  
Random Amplified Polymorphic Dna ◽  
Southeast Asian ◽  
Coi Gene ◽  
Cotton Leaf ◽  
Reading Frame ◽  
Genetic Lineages ◽  
The Family ◽  
Whitefly Vector

The genetic structure of field populations of begomoviruses and their whitefly vector Bemisia tabaci in Pakistan was analyzed. Begomoviruses and B. tabaci populations were sampled from different crops and weeds in different locations in Punjab and Sindh provinces, in areas where cotton leaf curl disease (CLCuD) occurs or does not occur. Phylogenetic analysis based on nucleotide sequences of the intergenic region in the viral DNA-A provided evidence of two clusters of isolates: viruses isolated from species in the family Malvaceae, and viruses isolated from other dicotyledon families. Analysis of the capsid protein (CP) open reading frame grouped isolates into three geographical clusters, corresponding to isolates collected in Punjab, Sindh, or both provinces. Random amplified polymorphic DNA analyses of the B. tabaci population showed that intrapopulation diversity was high at both the local and regional scales. Sequence analysis of the mitocondrial cytochrome oxydase I (mt COI) gene showed that the B. tabaci population was structured into at least three genetic lineages corresponding to the previously described Indian, Southeast Asian, and Mediterranean-African clades. The Indian clade was present only in Punjab, the Mediterranean-African only in Sindh, and the Southeast Asian in both provinces. B. tabaci haplotypes of the Indian clade were found only in the Punjab, where CLCuD occurs. Hence, the geographical distribution of virus and vector genotypes may be correlated, because similar phylogenetic relationships were detected for the viral CP and the vector mt COI genes.

Complete Mitochondrial Genome Sequence Analysis and Phylogenetic Location Determination of Hydropsyche Fryeri (Insecta: Trichoptera)

2021 ◽  
Author(s):  
Yimin Li ◽  
Honglin Qin ◽  
Xifa Zhong ◽  
Jingcai Huang ◽  
Yujun Wang ◽  
...  
Keyword(s):  
Mitochondrial Genome ◽  
Genome Sequence ◽  
Complete Mitochondrial Genome ◽  
Phylogenetic Tree Analysis ◽  
Protein Coding ◽  
Mitochondrial Genome Sequence ◽  
Complete Mitochondrial Genome Sequence ◽  
Location Determination ◽  
The Family

Abstract Hydropsyche fryeri belongs to the Trichopteridae family and builds nests in clean and unpolluted streams using stones. It also can be used as an indicator of water quality. Here, we describe the complete mitochondrial genome sequence of Hydropsyche fryeri. The mitochondrial genome is 15,676 bp long and contains 13 protein-coding genes, 22 tRNAs, 2 rRNAs and an AT-rich control region. Phylogenetic tree analysis shows that Hydropsyche fryeri is more closely related to the family Hydroptera than other Trichoptera.

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