scholarly journals Bioinformatics with basic local alignment search tool (BLAST) and fast alignment (FASTA)

2014 ◽  
Vol 6 (1) ◽  
pp. 1-6 ◽  
Author(s):  
S. Donkor Eric ◽  
T. K. D. Dayie Nicholas ◽  
K Adiku Theophilus
Keyword(s):  
Local Alignment ◽  
Search Tool

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 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 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 A Case Report on Genetic Analysis of Exon2 of Thyroid Transcription Factor 2 Gene in Congenital Hypothyroidism Patient

2021 ◽  
Vol 3 (2) ◽  
pp. 19-21
Author(s):  
Marjia Khatun ◽  
Laila Anjuman Banu
Keyword(s):  
Transcription Factor ◽  
Pediatric Patient ◽  
Congenital Hypothyroidism ◽  
Sanger Sequencing ◽  
Demographic Data ◽  
Local Alignment ◽  
Cycle Sequencing ◽  
Thyroid Transcription Factor ◽  
Search Tool ◽  
Information Database

A-3-year- old Bangladeshi pediatric patient named Tasin was presented with a diagnosed case of congenital hypothyroidism (CH). This type of hypothyroidism may occur due to the alteration in the nucleotide sequences of the Thyroid transcription factor 2 gene. Few studies are present on the genetic basis of this disease. CH is common in Bangladesh, may be due to geographical variation or other causes. Therefore, this study was conducted to identify whether there was any genetic alteration in the exon2 of Thyroid transcription factor 2 gene. With due procedure and permission from the guardian of the pediatric patient, socio-demographic data was collected. Isolation of DNA, quantitation and qualitation of DNA was ensured, polymerase chain reaction (PCR) was performed, the amplicons that was obtained from PCR; validated visually by gel electrophoresis methods; cycle sequencing was performed by Sanger sequencing. The chromatogram data that was obtained from Sanger sequencing was analyzed and compared with the National Center for Biotechnology Information database by Basic Local Alignment Search Tool search. Sanger sequencing revealed substitution (c.1051G>T) in the Sequence Tagged Site of the exon2 of Thyroid transcription factor 2 gene and this is new variants and not reported in National Center for Biotechnology Information database.

CaPSY1 gene plays likely the key role in carotenoid metabolism of pepper (Capsicum annuum) at ripening

2021 ◽  
Vol 48 (2) ◽  
pp. 141
Author(s):  
Xiaochun Wei ◽  
Chunyang Meng ◽  
Yuxiang Yuan ◽  
Ujjal Kumar Nath ◽  
Yanyan Zhao ◽  
...  
Keyword(s):  
Developmental Stages ◽  
Carotenoid Biosynthesis ◽  
Local Alignment ◽  
Fruit Colour ◽  
Virus Induced Gene Silencing ◽  
Carotenoid Metabolism ◽  
Pepper Fruit ◽  
Search Tool ◽  
Pepper Genome ◽  
Aba Content

Phytoene synthase (PSY) is the first committed enzyme in carotenoid biosynthesis, which plays important role in ripen fruit colour. However, the roles of CaPSY genes are not explained detail in ripen pepper fruit colour. In this study, three CaPSY genes (CaPSY1, CaPSY2 and CaPSY3) were identified through basic local alignment search tool (BLAST) in pepper genome. Among them, CaPSY1 was predicted as putative candidate based on relative expression values using five developmental stages of fruit in Zunla-1 cultivar and also in ripen fruits of five contrasting pepper lines. The CaPSY1 was characterised functionally through virus-induced gene silencing (VIGS) in ripen fruits and overexpression in Arabidopsis thaliana (L.) Heynh. Silencing of CaPSY1 gene altered colour with increased lutein and decreased zeaxanthin content in pepper fruits. The transgenic Arabidopsis line CaPSY1 gene showed higher expression of PSY1 gene compared with WT and dwarf phenotype due to reduction of GA3 (gibberellic acid) and higher abscisic acid (ABA) content. Our results confirmed that CaPSY1 gene involved in carotenoid metabolism in ripen pepper fruit and provide clue to develop bright red coloured pepper lines through breeding.

scholarly journals Novel Single Hematophagous Insect RNA Detection Method Supports Its Use as Sentinels to Survey Flaviviruses Circulation

2020 ◽  
Author(s):  
Juliana Sá Teles de Oliveira Molina ◽  
Andreia Moreira dos Santos Carmo ◽  
Gabriel Lopes Pereira ◽  
Leticia Abrantes de Andrade ◽  
Felipe Trovalim Jordão ◽  
...  
Keyword(s):  
Control Strategies ◽  
Phylogenetic Analyses ◽  
Rna Extraction ◽  
Local Alignment ◽  
Rna Detection ◽  
Public Park ◽  
Preventive Control ◽  
Culex Flavivirus ◽  
Search Tool ◽  
Pcr Targeting

Anthropogenic actions, including deforestation, disorganized urbanization, and globalization, contribute to emergence and reemergence of arboviruses worldwide, where Flavivirus is the most prevalent, and its continuous monitoring can help in preventive control strategies. Thus, the aim of this study was to detect flavivirus RNA in single hematophagous insects, which are used as sentinels. Total RNA was extracted from six Aedes aegypti stored since 2003 and from 100 Culicidae and collected through CDC trap in a public park of a Brazilian Northwest city of São Paulo State. Flavivirus was detected through RT/PCR targeting 230–250 bp of the RNA polymerase coding sequence (NS5). PCR amplicons were sequenced by Sanger method, used in comparative analysis over Basic Local Alignment Search Tool (BLAST) in GenBank, and subjected to Neighbor-Joining phylogenetic analyses. Efficiency of Flavivirus diagnosis was confirmed by detection of Dengue virus serotype 2 in Ae. aegypti. From the 100 collected insects, 19 were positive for Culex flavivirus (CxFV). NS5 partial sequence phylogenetic analysis clustered all CxFV in one branch separated from vertebrate flaviviruses, being applicable to the identification of Flavivirus species. The dipteran RNA extraction methodology described in this work supports detection of flaviviruses in single insects maintained in 80% ethanol, which can be used to constant arbovirus surveillance.

scholarly journals Trans-Species Polymorphism in Mitochondrial Genome of Camarodont Sea Urchins

Genes ◽  
2019 ◽  
Vol 10 (8) ◽  
pp. 592
Author(s):  
Evgeniy S. Balakirev
Keyword(s):  
Sea Urchins ◽  
Stop Codon ◽  
Global Ocean ◽  
Abrupt Climate Change ◽  
Local Alignment ◽  
Codon Reassignment ◽  
Length Difference ◽  
Search Tool ◽  
Alternative Hypotheses ◽  
Mesocentrotus Nudus

Mitochondrial (mt) genomes of the sea urchins Strongylocentrotus intermedius and Mesocentrotus nudus demonstrate the identical patterns of intraspecific length variability of the ND6 gene, consisting of 489 bp (S variant) and 498 bp (L variant), respectively. For both species, the ND6 length difference is due to the 488A>G substitution, which changes the stop codon TAG in S variant for a tryptophan codon TGG in L variant and elongates the corresponding ND6 protein by three additional amino acids, Trp-Leu-Trp. The phylogenetic analysis based on mt genomes of sea urchins and related echinoderm groups from GenBank has shown the S and L ND6 variants as shared among the camarodont sea urchins; the rest of the echinoderms demonstrate the S variant only. The data suggest that the ND6 488A>G substitution can be the first example of the trans-species polymorphism in sea urchins, persisting at least since the time of the Odontophora diversification at the Eocene/Oligocene boundary (approximately 34 million years ago), which was characterized by an abrupt climate change and significant global ocean cooling. Alternative hypotheses, including the convergent RNA editing and/or codon reassignment, are not supported by direct comparisons of the ND6 gene sequences with the corresponding transcripts using the basic local alignment search tool (BLAST) of full sea urchin transcriptomes.

scholarly journals Molecular characterisation of Mycoplasma species isolated from the genital tract of Dorper sheep in South Africa

2015 ◽  
Vol 86 (1) ◽  
Author(s):  
Habu A. Kalshingi ◽  
Anna-Mari Bosman ◽  
Johan Gouws ◽  
Moritz Van Vuuren
Keyword(s):  
South Africa ◽  
Genital Tract ◽  
The United States ◽  
Mycoplasma Species ◽  
Local Alignment ◽  
Large Colony ◽  
Mycoplasma Mycoides ◽  
Search Tool ◽  
Dorper Sheep ◽  
Arcanobacterium Pyogenes

Biochemical and molecular analysis were conducted on 34 strains of Mycoplasma species isolated between 2003 and 2009 from the genital tract of clinically healthy Dorper sheep and sheep with ulcerative vulvitis and balanitis. Earlier publications identified the causative agent as Mycoplasma mycoides mycoides large colony (MmmLC) and Arcanobacterium pyogenes. The aims of the study were to characterise Mycoplasma species isolated from the genital tract of Dorper sheep with polymerase chain reaction assay, cloning and gene sequencing. Basic Local Alignment Search Tool (BLAST) results revealed six predominant Mycoplasma species: Mycoplasma arginini, Mycoplasma bovigenitalium, Arcanobacterium laidlawii, MmmLC, Mycoplasma sp. ovine/caprine serogroup II and M. canadense. Sequencing of the 34 isolates were analysed using phylogenetic methods, and 18 (50%) were identified as M. arginini with 99% – 100% similarity to M. arginini from England and Sweden. Six isolates showed 99% similarity to M. bovigenitalium strains from Turkey and Germany. Two isolates had 99% similarity to an M. sp. ovine/caprine sero group II from the United Kingdom. BLAST for two isolates revealed 99% similarity to Acholeplasma laidlawii from India, another two were 99% similar to MmmLC strain from Sweden, two showed 98% similarity to Mycoplasma sp. Usp 120 from Brazil, and two isolates have a 97% – 99% similarity to M. mm. Jcv1 strain from the United States of America. Finally, one isolate showed similarity of 99% to Mycoplasma canadense strain from Italy. The findings support the hypothesis that ulcerative vulvitis and balanitis of Dorper sheep in South Africa (SA) is a multifactorial disease with involvement of different Mycoplasma species.

Genotyping of Acanthamoeba Species Isolated from Keratitis Patients by PCR Sequencing Methods in Tehran, Iran

2019 ◽  
Author(s):  
Tooran Nayeri Chegeni ◽  
Fatemeh Ghaffarifar ◽  
Majid Pirestani ◽  
Fariba Khoshzaban ◽  
Abdolhosein Dalimi Asl ◽  
...  
Keyword(s):  
Contact Lenses ◽  
Pcr Amplification ◽  
Acanthamoeba Keratitis ◽  
Local Alignment ◽  
Sequencing Analysis ◽  
Search Tool ◽  
Skin Nodules ◽  
Acanthamoeba Species ◽  
Eye Clinic

  Background and Aims: Amoebae of the genus Acanthamoeba are unicellular amphizoic opportunistic pathogens that may cause fatal granulomatous encephalitis, eye keratitis, amebic pneumonitis and skin nodules as well as abscesses in humans and animals. Acanthamoeba keratitis is caused by trauma to the eye, contaminated cleaning solutions and the use of contact lenses. The aim of the present study was to identify the genotypes of Acanthamoeba in all patients with a clinical diagnosis of Acanthamoeba keratitis referring to eye clinic in Tehran using polymerase chain reaction (PCR).  Materials and Methods: In this study, samples were collected from 35 patients who had referred to the eye clinic and were cultured on 1.5% non-nutrient agar. DNA was extracted, and then PCR amplification was performed using genus specific primers. Sequencing analysis and basic local alignment search tool search were conducted to determine the genotypes. Phylogenetic tree was generated using maximum likely algorithm in phylogenetic program MEGA version 6.  Results: Eight cases were positive for Acanthamoeba using genus specific primer pairs. All specimens were reported as genotype T4. Conclusions: Determination of genotypes showed all isolates belonging to genotype T4; this abundance may be due to its higher prevalence in the environment or its greater virulence. However, further analysis of clinical and environmental samples is necessary to clarify this property.   

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