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Phylogenetics software

Dmitry Penzar, Mikhail Krivozubov, Sergey Spirin
BACKGROUND: Many algorithms and programs are available for phylogenetic reconstruction of families of proteins. Methods used widely at present use either a number of distance-based principles or character-based principles of maximum parsimony or maximum likelihood. RESULTS: We developed a novel program, named PQ, for reconstructing protein and nucleic acid phylogenies following a new character-based principle. Being tested on natural sequences PQ improves upon the results of maximum parsimony and maximum likelihood...
October 12, 2018: BMC Bioinformatics
Jonathan N Wells, Joseph A Marsh
Reconstructing evolutionary relationships in repeat proteins is notoriously difficult due to the high degree of sequence divergence that typically occurs between duplicated repeats. This is complicated further by the fact that proteins with a large number of similar repeats are more likely to produce significant local sequence alignments than proteins with fewer copies of the repeat motif. Furthermore, biologically correct sequence alignments are sometimes impossible to achieve in cases where insertion or translocation events disrupt the order of repeats in one of the sequences being aligned...
2019: Methods in Molecular Biology
Mariano Avino, Art F Y Poon
The comparative study of homologous proteins can provide abundant information about the functional and structural constraints on protein evolution. For example, an amino acid substitution that is deleterious may become permissive in the presence of another substitution at a second site of the protein. A popular approach for detecting coevolving residues is by looking for correlated substitution events on branches of the molecular phylogeny relating the protein-coding sequences. Here we describe a machine learning method (Bayesian graphical models) implemented in the open-source phylogenetic software package HyPhy, http://hyphy...
2019: Methods in Molecular Biology
Michael Hall, Robert G Beiko
Microbial marker-gene sequence data can be used to generate comprehensive taxonomic profiles of the microorganisms present in a given community and for other community diversity analyses. The process of going from raw gene sequences to taxonomic profiles or diversity measures involves a series of data transformations performed by numerous computational tools. This includes tools for sequence quality checking, denoising, taxonomic classification, alignment, and phylogenetic tree building. In this chapter, we demonstrate how the Quantitative Insights Into Microbial Ecology version 2 (QIIME2) software suite can simplify 16S rRNA marker-gene analysis...
2018: Methods in Molecular Biology
Kevin Egan, Des Field, R Paul Ross, Paul D Cotter, Colin Hill
The thermophilic, endospore-forming genus of Geobacillus has historically been associated with spoilage of canned food. However, in recent years it has become the subject of much attention due its biotechnological potential in areas such as enzyme and biofuel applications. One aspect of this genus that has not been fully explored or realized is its use as a source of novel forms of the ribosomally synthesized antimicrobial peptides known as bacteriocins. To date only two bacteriocins have been fully characterized within this genus, i...
2018: Frontiers in Microbiology
Haohui Deng, Shuzhen Liang, Huiyuan Liu, Min Xu, Li Zhuo, Hongbo Gao
The dominant human immunodeficiency virus type 1 (HIV-1) subtypes are CRF01_AE, CRF07_BC and CRF08_BC in Guangdong Province, China. In this study, we report a unique recombinant form (URF) of HIV-1 that was identified in an HIV/hepatitis B virus (HBV)/hepatitis C virus (HCV) triple-infected patient who was an intravenous drug user (IDU) in Heyuan City, Guangdong Province. The near full-length genome was amplified, and the PCR products were sequenced by Sanger's method. The Recombination Identification Program (RIP 3...
October 5, 2018: Archives of Virology
Andrew E Schriefer, Paul F Cliften, Matthew C Hibberd, Christopher Sawyer, Victoria Brown-Kennerly, Lauren Burcea, Elliott Klotz, Seth D Crosby, Jeffrey I Gordon, Richard D Head
Metagenomic sequencing of bacterial samples has become the gold standard for profiling microbial populations, but 16S rRNA profiling remains widely used due to advantages in sample throughput, cost, and sensitivity even though the approach is hampered by primer bias and lack of specificity. We hypothesized that a hybrid approach, that combined targeted PCR amplification with high-throughput sequencing of multiple regions of the genome, would capture many of the advantages of both approaches. We developed a method that identifies and quantifies members of bacterial communities through simultaneous analysis of multiple variable regions of the bacterial 16S rRNA gene...
September 29, 2018: Journal of Microbiological Methods
Julie Yamaguchi, Ana Olivo, Oliver Laeyendecker, Kenn Forberg, Nicaise Ndembi, Dora Mbanya, Lazare Kaptue, Thomas C Quinn, Gavin A Cloherty, Mary A Rodgers, Michael G Berg
Background: Global surveillance of viral sequence diversity is needed to keep pace with the constant evolution of HIV. Recent next generation sequencing (NGS) methods have realized the goal of sequencing circulating virus directly from patient specimens. Yet, a simple, universal approach that maximizes sensitivity and sequencing capacity remains elusive. Here we present a novel HIV enrichment strategy to yield near complete genomes from low viral load specimens. Methodology: A non-redundant biotin-labeled probe set (HIV-xGen; n = 652) was synthesized to tile all HIV-1 (groups M, N, O, and P) and HIV-2 (A and B) strains...
2018: Frontiers in Microbiology
J Bradley Reil, Camiel Doorenweerd, Michael San Jose, Sheina Sim, Scott Geib, Daniel Rubinoff
Biological control agents have several advantages over chemical control for pest management, including the capability to restore ecosystem balance with minimal non-target effects and a lower propensity for targets to develop resistance. These factors are particularly important in the invasive species control. The coconut rhinoceros beetle (Oryctes rhinoceros Linnaeus) is a major palm pest that invaded many Pacific islands in the early 20th century through human-mediated dispersal. Application of the Oryctes nudivirus in the 1960's successfully halted the beetle's first invasion wave and made it a textbook example of successful biological control...
September 25, 2018: Molecular Ecology
Arpit Saxena, Sanchay K Biswas, Karam Chand, Jishnu Naskar, Ankita Chauhan, Gulam Mohd, Neha Tewari, Kurat-Ul-Ain, Muthannan A Ramakrishnan, Awadh Bihari Pandey
Aim: The aim of the study was to characterize bluetongue virus serotype 16 (BTV-16), recently isolated from different states of India. The evolutionary relationship of newly isolated BTV-16 and previously reported Indian and global BTV-16 isolates were compared using molecular analysis. Materials and Methods: In the present study, five (n=5) BTV-16 isolates were used to amplify gene segment-2 and segment-6 encoding the outer capsid proteins VP2 and VP5 , respectively...
August 2018: Veterinary World
Guy Baele, Simon Dellicour, Marc A Suchard, Philippe Lemey, Bram Vrancken
Time-stamped, trait-annotated phylogenetic trees built from virus genome data are increasingly used for outbreak investigation and monitoring ongoing epidemics. This routinely involves reconstructing the spatial and demographic processes from large data sets to help unveil the patterns and drivers of virus spread. Such phylodynamic inferences can however become quite time-consuming as the dimensions of the data increase, which has led to a myriad of approaches that aim to tackle this complexity. To elucidate the current state of the art in the field of phylodynamics, we discuss recent developments in Bayesian inference and accompanying software, highlight methods for improving computational efficiency and relevant visualisation tools...
September 21, 2018: Current Opinion in Virology
Nicole Huber, Walther Parson, Arne Dür
Mitochondrial DNA (mtDNA) variation is being reported relative to the corrected version of the first sequenced human mitochondrial genome. A review of the existing literature across disciplines that employ mtDNA demonstrates that insertions and deletions are not reported in a standardized way. This may lead to false exclusions of identical sequences, unidentified matches in missing persons mtDNA databases, biased mtDNA database frequency estimates and overestimation of the genetic evidence. Seven years ago we introduced alignment-free database search software (SAM) and implemented it into the mtDNA database EMPOP (https://empop...
September 9, 2018: Forensic Science International. Genetics
Jian-Ning Chen, Lu Zhou, Xin-Min Qiu, Ri-Hong Yang, Jing Liang, Yu-Hang Pan, Hai-Feng Li, Guo-Rong Peng, Chun-Kui Shao
About 10 % of gastric carcinoma worldwide is associated with EBV, which is defined as EBV-associated gastric carcinoma (EBVaGC). To date, EBV sequence data from EBVaGC in Guangdong, China, an endemic area of nasopharyngeal carcinoma (NPC), are not available. In the present study, two EBV genomes from EBVaGC specimens from Guangdong (designated as GDGC1 and GDGC2) were determined by next-generation sequencing, de novo assembly and joining of contigs by Sanger sequencing. In addition, we sequenced EBV from two Korean EBVaGC cell lines, YCCEL1 and SNU-719...
September 21, 2018: Journal of Medical Microbiology
Lin Yin, Fang Liu, Changcheng Guo, Qiong Wang, Ke Pan, Liangbi Xu, Yan Xiong, Yingting Chen, Zhenghong Chen
The present study aimed to investigate the virulence diversity of Helicobacter pylori (H. pylori) in major ethnic groups residing in Guizhou province, China, and its association with clinical outcomes. Gastric mucosal biopsies were collected from the pylorus of patients with gastrointestinal disorders. H. pylori was identified by colonial morphology, Gram staining, a urease test and H. pylori‑specific 16S rRNA gene fragment PCR amplification. DNA was extracted from pure culture and used for virulence gene analysis...
September 5, 2018: Molecular Medicine Reports
Bin Yan, Xiafei Liu, Junyuan Wu, Shanshan Zhao, Wumei Yuan, Baoju Wang, Hazi Wureli, Changchun Tu, Chuangfu Chen, Yuanzhi Wang
Cystic echinococcosis (CE) caused by E. granulosus is a serious helminthic zoonosis in humans, livestock and wildlife. Xinjiang is one of high endemic province for CE in China. A total of 55 sheep and cattle livers containing echinococcal cysts were collected from slaughterhouses in Changji and Yining City, northern region of Xinjiang. PCR was employed for cloning 2 gene fragments, 12S rRNA and CO1 for analysis of phylogenetic diversity of E. granulosus. The results showed that all the samples collected were identified as G1 genotype of E...
August 2018: Korean Journal of Parasitology
Wei Liang, Feng Cai, Liang Yang, Zhe Zhang, Zhicheng Wang
Background: The para-Bombay phenotype is characterized by a lack of ABH antigens on red cells, but ABH substances are found in saliva. Molecular genetic analysis was performed for seven Chinese individuals serologically typed as para-Bombay in Blood Station Center of Ningbo, Zhejiang Province, Ningbo, China from 2011 to 2014. Methods: RBCs' phenotype was characterized by standard serologic technique. Genomic DNA was sequenced with primers that amplified the coding sequence of α (1, 2)-fucosyltransferase genes FUT1 (or H ) and FUT2 (or Se ), respectively...
August 2018: Iranian Journal of Public Health
Chien-Hsun Huang, Shiao-Wen Li, Lina Huang, Koichi Watanabe
Lactobacillus casei, Lactobacillus paracasei , and Lactobacillus rhamnosus are phenotypically and genotypically closely related, and together comprise the L. casei group. Although the strains of this group are commercially valuable as probiotics, the taxonomic status and nomenclature of the L. casei group have long been contentious because of the difficulties in identifying these three species by using the most frequently used genotypic methodology of 16S rRNA gene sequencing. Long used as the gold standard for species classification, DNA-DNA hybridization is laborious, requires expert skills, and is difficult to use routinely in laboratories...
2018: Frontiers in Microbiology
Ivana Piližota, Clément-Marie Train, Adrian Altenhoff, Henning Redestig, Christophe Dessimoz
Motivation: As the time and cost of sequencing decrease, the number of available genomes and transcriptomes rapidly increases. Yet the quality of the assemblies and the gene annotations varies considerably and often remains poor, affecting downstream analyses. This is particularly true when fragments of the same gene are annotated as distinct genes, which may cause them to be mistaken as paralogs. Results: In this study, we introduce two novel phylogenetic tests to infer non-overlapping or partially overlapping genes that are in fact parts of the same gene...
September 1, 2018: Bioinformatics
Amir Pouremamali, Manoochehr Makavndi, Alireza Samarbafzadeh, Niloofar Neisi, Mojtaba Rasti, Ahmad Shamsizadeh, Ali Teimoori, Mehrdad Sadeghi Haj, Roohangiz Nashibi, Shokrallah Salmanzadeh, Roya Nikfar, Rahim Soleimani, Abdolnabi Shabani
  Background: Acute respiratory infection result in high mortality and morbidity worldwide. There are several viral factors that originate respiratory diseases among them Enteroviruses(EVs) and Human Rhinoviruses(HRVs) can be mentioned. HRVs and EVs belong to Picornaviridae family and they have been recently classified under Enteroviruses. The pattern of respiratory infections generating organisms varies according to geographical locations. Therefore, it seems necessary to organize an appropriate plan to manage common viral diseases exclusively about Rhinoviruses and Enteroviruses...
2018: Epidemiologie, Mikrobiologie, Imunologie
Bruno Francisco Sant'Anna-Santos, Samuel Alves Dos Santos, Elaine L P Nunes, Dayana Maria Teodoro Francino, Wellington Geraldo Oliveira Carvalho Júnior
Butia is a neotropical genus whose identification is based mostly on characters from external morphology, which are sometimes variable or inadequate for species differentiation. We aimed to verify if leaf anatomy of 18 Butia species brings new characters suitable for species identification and if it corroborates the phylogenetic relationship within the genus. Moreover, we propose an anatomical key to assist in species identification. Pinnae were collected and subjected to the usual techniques for light and scanning electron microscopies...
August 2018: AoB Plants
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