Use of the “DNAChecker” Algorithm for Improving Bioinformatics Research

Bhat, Nausheen; Wijaya, Ezra B.; Parikesit, Arli Aditya

doi:10.7454/mst.v23i2.3488

Cited by 6 publications

(7 citation statements)

References 17 publications

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“…BLAST-QC's design for easy integration into high-throughput workflows and pipelines resonates with our use of Biopython, which similarly provides a lightweight and portable solution for BLAST result analysis [24]. Moreover, the 'DNAChecker' algorithm's focus on assessing sequence quality before BLAST analysis complements our methodology, ensuring the effectiveness of the BLAST results by pre-screening the input sequences [25]. This pre-analysis step is crucial, given the open-platform nature of biological databases that often accept sequences with varying quality.…”

Section: Blast Parameter Optimization With Algorithmic Efficiencymentioning

confidence: 92%

AI-Enabled Pipeline for Virus Detection, Validation, and SNP Discovery from Next-Generation Sequencing Data

Ghorbani,

Guzzi,

Rostami

2024

Preprint

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The rapid and accurate detection of viruses and the discovery of single nucleotide polymorphisms (SNPs) are crucial for disease management and understanding viral evolution. In this study, a pipeline for virus detection, validation, and SNP discovery from next-generation sequencing (NGS) data is presented. By integrating state-of-the-art bioinformatics tools with artificial intelligence, the pipeline processes raw sequencing data to identify viral sequences with high accuracy and sensitivity. Before aligning the reads to the reference genomes, quality control measures and adapter trimming are performed to ensure the integrity of the data. Unmapped reads are subjected to de novo assembly to reveal novel viral sequences and genetic elements. The effectiveness of the pipeline is demonstrated by the identification of virus sequences, illustrating its potential for the detection of known and emerging pathogens. SNP discovery is performed using a custom Python script that compares the entire population of sequenced viral reads to a reference genome. This approach provides a comprehensive overview of viral genetic diversity and identifies dominant variants and a spectrum of genetic variations. The robustness of the pipeline is confirmed by the recovery of complete viral sequences, which improves our understanding of viral genomics. This study highlights the synergy between traditional bioinformatics techniques and modern approaches, providing a robust tool for analyzing viral genomes and contributing to the broader field of viral genomics.

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Section: Blast Parameter Optimization With Algorithmic Efficiencymentioning

confidence: 92%

AI-Enabled Pipeline for Virus Detection, Validation, and SNP Discovery from Next-Generation Sequencing Data

Ghorbani,

Guzzi,

Rostami

2024

Preprint

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“…Qualities of the DNA sequences were checked and Phred scores above 30 were considered for downstream analysis. Each strand was manually edited and trimmed using Finch TV to generate consensus sequences [19]. Generated DNA sequences were submitted to the NCBI GenBank and the following accession numbers were assigned.…”

Section: Sequence Analysismentioning

confidence: 99%

Integrated morphometric and molecular approaches to screen hybrid from wild Labeo rohita and Catla catla parent populations

Lenka,

Singh,

Ghosh

et al. 2024

Preprint

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Background: Interspecific hybrids of rohu (Labeo rohita) and catla (Catla catla) are common, especially in India due to constrained breeding. These hybrids must segregate from their wild parents as part of conservational strategies. In this study, we screen the hybrid from wild Labeo rohita and Catla catla parents using both morphometric and molecular approaches. Methods & Results:The carp samples were collected from Jharkhand and West Bengal, India. The correlation and regression analysis of morphometric features are considered superficial but could be protracted statistically by clustering analysis and further consolidated by nucleotide variations of one mitochondrial and one nuclear gene to differentiate hybrids from their parents. Out of twenty morphometric features, six were used for clustering analysis. The clustering analysis showed discrete separation among rohu, catla, and their hybrids when the data points were plotted in a low-dimensional 2-D plane using the first 2 principal components. Out of forty selected SNP positions of the COX1 gene, hybrid showed 100% similarity with catla. Concerning SNP similarity of the 18S rRNA nuclear gene, the hybrid showed 100 % similarity with rohu but not with catla thus exhibiting its most probable paternal origin as rohu that confirms their parental source of sperm (rohu) and ovum (catla). Conclusions: Along with clustering analysis the SNP comparison study together points towards strong evidence of interspecific hybridization between rohu and catla, as these hybrids share both morphological and molecular differences with either parent. However, this screening process will be further consolidated by analysing more sequences.

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“…The Sanger method (1977) was used for DNA sequencing, performed by a sequencing company with the PCR products sent to First Base, Malaysia. The resulting chromatograms were analyzed using bioinformatics software, including Finch TV (Bhat et al 2019), DNA Baser Assembler v5.15.0, Clustal X Version 2.1 (Ferrari and Patrizio 2021), BioEdit Version 7.0.5.3, and MEGA 6.0 (Tamura et al 2013). DNA sequences obtained were used to determine genetic variation, nucleotide and amino acid composition, genetic distance, and relationships within the COX1 gene.…”

Section: Sequencingmentioning

confidence: 99%

Morphological and molecular characteristics of Donax incarnatus (Bivalvia: Donacidae) from Badur Beach, Madura Island, Indonesia based on the COX1 gene

WIJAYA,

AMBARWATI,

RAHAYU

2023

Biodiversitas

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Abstract. Wijaya CB, Ambarwati R, Rahayu DA. 2023. Morphological and molecular characteristics of Donax incarnatus (Bivalvia: Donacidae) from Badur Beach, Madura Island, Indonesia based on the COX1 gene. Biodiversitas 24: 2805-2813. Donacidae, a family of marine bivalve mollusks, has a high diversity of morphological traits, including shape and color pattern variations. However, these variations often led to errors in morphological identification, necessitating the use of molecular identification methods for accurate species identification and support. This study aims to analyze the morphological and molecular characteristics of Donax incarnatus Gmelin, 1791 collected from Badur Beach of Madura Island, Sumenep District, East Java Province, Indonesia, using the COX1 gene as a molecular marker. Morphological characterization was conducted through qualitative and quantitative observations, while sequencing results were analyzed using bioinformatics software. The results showed that the exterior color of D. incarnatus has three morphological variations, namely purple-black (OQ692130.1), yellowish orange (OQ692131.1), and white (OQ692132.1). Molecular characterization indicated that the similarity value of D. incarnatus with these variations ranged from 96.06% to 99.61%. At the same time, the alignment results of all samples with reference species and outgroups obtained five variations of nucleotide bases. The average genetic distance between D. incarnatus and the in group was 0.01. The phylogenetic tree results obtained using Neighbor-Joining (NJ) and Maximum Likelihood (ML)methods were categorized into two subclusters: D. incarnatus species from Thailand and the study sample from Badur Beach, Madura Island, Indonesia, were placed in the same cluster.

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Use of the “DNAChecker” Algorithm for Improving Bioinformatics Research

Cited by 6 publications

References 17 publications

AI-Enabled Pipeline for Virus Detection, Validation, and SNP Discovery from Next-Generation Sequencing Data

AI-Enabled Pipeline for Virus Detection, Validation, and SNP Discovery from Next-Generation Sequencing Data

Integrated morphometric and molecular approaches to screen hybrid from wild Labeo rohita and Catla catla parent populations

Morphological and molecular characteristics of Donax incarnatus (Bivalvia: Donacidae) from Badur Beach, Madura Island, Indonesia based on the COX1 gene

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