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Methods for Outbreaks Using Genomic Data
Published in Leonhard Held, Niel Hens, Philip O’Neill, Jacco Wallinga, Handbook of Infectious Disease Data Analysis, 2019
Don Klinkenberg, Caroline Colijn, Xavier Didelot
Two of the most frequently used methods to visualize and analyze sequence data are the Minimum Spanning Tree (MST) and the Neighbor Joining (NJ) algorithm. Both methods build a tree from the distance matrix rather than from the complete sequences. The main difference in the result is that MST makes a tree in which every node represents one or more samples, whereas the NJ algorithm returns a phylogenetic tree, in which the samples are only located on the tip nodes, and the internal nodes represent putative ancestors.
DNA barcoding
Published in C. P. Khare, Evidence-based Ayurveda, 2019
BLAST (Basic Local Alignment Search Tool) search was performed against GenBank3 and BOLD (Barcode of Life Database) databases. TaxonDNA v. 1.6.2 (http://taxondna.sf.net/) was used to calculate pairwise divergence. Phylogenetic tree based on Neighbor-Joining (NJ) method was constructed using MEGA version 5.1 Best match method was used for the authentication of the raw drug market samples.4 Unmatched samples were analyzed by BLAST search against the NCBI nucleotide database and BOLD database.
Mycobacterium
Published in Dongyou Liu, Laboratory Models for Foodborne Infections, 2017
Flábio R. de Araújo, Nalvo F. Almeida
A second tree (data not shown) was obtained by using this matrix as input for a neighbor-joining distance-based phylogeny method [73]. The distance-based topology obtained completely agrees with the tree shown in Figure 12.1.
Epidemiological characteristics of acute hepatitis A, 2013–2016: a cross-sectional study in Morocco
Published in Infectious Diseases, 2023
Adnane Karami, Raouia El Fihry, Asmaa Haddaji, Fatima-Zahra Jadid, Imane Zaidane, Hajar Chihab, Ahd Ouladlahsen, Mohamed Tahiri, Pascal Pineau, Khadija Akarid, Soumaya Benjelloun, Sayeh Ezzikouri
The entire VP3, VP1 and VP1-2A junction region nucleotide sequences of the HAV genomes were compared with HAV sequences deposited in GenBank using the BLAST program (https://www.ncbi.nlm.nih.gov/blast/), edited with BioEdit and aligned with reference strains from GenBank representing different genotypes and geographical areas using MEGA version 11 (Molecular Evolutionary Genetics Analysis 11.0,www.megasoftware.net) [26,27]. The obtained VP1/VP2A junction sequences have been deposited into GenBank under the following accession numbers [OQ341470 - OQ341485] (Supplementary Table I). Neighbor-joining (NJ) tree was constructed using the Kimura two-parameter method. The reliability was assessed by bootstrap resampling (1000 pseudo-replicas). Only bootstrap values above 80% are shown on the phylogenetic trees. Tree editing was done using the iTOL software version V5 [28]. HAV reference sequences used for comparisons were obtained from GenBank.
Identification, characterization, and molecular phylogeny of scorpion enolase (Androctonus crassicauda and Hemiscorpius lepturus)
Published in Toxin Reviews, 2023
Elham Pondehnezhadan, Atefeh Chamani, Fatemeh Salabi, Reihaneh Soleimani
Conservation or divergence of enolase genes in arthropods and insects was determined by homology searches of enolase protein sequences obtained from A. crassicauda and H. lepturus with other scorpion species, arthropods, and insects listed in Table 1. The alignment was made online with NCBI (https://blast.ncbi.nlm.nih.gov/https://www.ebi.ac.uk/Tools/msa/mafft/) and edited in the Bio Edit software. Multiple sequence alignments of closely-related protein sequences to the candidate protein of A. crassicauda and H. lepturus scorpions were also performed using the Clustal W alignment tool (Thompson et al. 1994). The alignment results were used to estimate a consensus phylogenetic tree with the MEGA X package (Kumar et al. 2018). An unrooted phylogenetic tree was created for the Neighbor-Joining (NJ) method. The reliability of branching was analyzed using bootstrap re-sampling with 1000 bootstrap replicates and Jones-Taylor-Thornton (JTT) model with a “Pairwise Deletion” option.
New insights about scorpion venom hyaluronidase; isoforms, expression and phylogeny
Published in Toxin Reviews, 2023
In this study, homologs of hyaluronidase were searched using blastp. For this purpose, the relevant isoform sequences with accurate constitutive exons, which encode hyaluronidase from A. crassicauda and H. lepturus scorpions, were aligned with submitted Hyal protein sequences in NCBI. The alignment was made online with NCBI (https://www.ebi.ac.uk/Tools/msa/mafft/), and edited in BioEdit. A total of 18 hyaluronidase sequences were used for phylogenetic reconstruction. The amino acid sequences of the resulting Hase from A. crassicauda and H. lepturus scorpions plus the other previously reported sequences of scorpion toxins, Apis mellifera, and spider specific for hyaluronidase, were further aligned using the ClustalW alignment tool in the MEGA package (Version X) (Kumar et al. 2018). The multiple alignments obtained were used to estimate a consensus phylogenetic tree with MEGA X (Kumar et al. 2018). The neighbor Joining (NJ) method was used for estimating phylogenetic trees, with the bootstrap value set to 1000.