Phylogenetic sequence alignment. Medical search. Frequent questions

Over the last decade or so, new multiple sequence alignment methods have been developed to improve comparative analyses of protein structure, but these new methods have not been typically used in phylogenetic analyses. (illinois.edu)
In relation to the wide present offer of tools and algorithms for phylogenetic analyses, SeaView is especially useful for teaching and for occasional users of such software. (hal.science)
Genetic and phylogenetic analyses revealed that this Sanmenxia H5N1 virus was a novel reassortant, possessing a Clade 2.3.2.1c HA gene and a H9N2-derived PB2 gene. (nature.com)
HDV genotypes were characterized by Next-generation sequencing (NGS), followed by phylogenetic analyses. (researchsquare.com)
Phylogenetic analyses indicated that HDV-2 genotype being the predominant genotype, other HDV genotypes were not observed. (researchsquare.com)
In a nutshell, this workbench simplifies first phylogenetic analyses to a few clicks. (jove.com)
core algorithms of sequence analyses and phylogeny construction. (orientblackswan.com)
C. apodocarpa, C. caespiticia, and C. petrophila) is revised using morphological, chemical, and ecological data in combination with molecular phylogenetic analyses of ITS1, 5.8S, and ITS2 sequence data. (datadryad.org)
In addition, no phylogenetic structure is detected for the chemical races of C. petrophila with and without fumarprotocetraric acid, based on the markers used in these analyses. (datadryad.org)
Nexus formatted alignment of nuITS sequences used for molecular phylogenetic analyses in this study. (datadryad.org)
Molecular phylogenetic analyses indicate an intermediate position for T . equi between B . bovis and Theileria spp. (biomedcentral.com)
It provides a wide range of options that were designed to facilitate standard phylogenetic analyses. (debian.net)

They are classified into at least three species, HRV-A, HRV-B and HRV-C, which are characterized by sequencing the 5′ untranslated region (UTR) or the VP4/VP2 region of the genome. (plos.org)
We examined possible origins of this outbreak by performing phylogenetic analysis of genome sequences of MPXV isolates from the outbreak in Sudan and from differing localities. (cdc.gov)
7 ) investigated phylogenetic relationships between MPXV isolates by examining 5 whole-genome sequences. (cdc.gov)
It integrates confirmed Covid-19 cases, deaths, Sars-CoV-2 reference genome and nucleotide sequences from isolates deposited in Genbank. (elixir-europe.org)
Using genome-wide analysis, 20 GASA s were identified in lettuce including, three groups of LsGASA proteins based on the phylogenetic analysis. (biomedcentral.com)
A total of 26 GA2ox sequences were also retrieved from potato genome database and analysed. (bvsalud.org)
This study examined the added value of whole genome sequencing (WGS) for investigating a non-point source outbreak of Salmonella ser. (who.int)
2 Whole genome England and Central Coast local health districts of sequencing (WGS) is a high-resolution typing method NSW. (who.int)
This placement makes the pygmy right whale genome an interesting target to update the complex phylogenetic past. (lu.se)
This placement makes the pygmy right whale genome an interesting target to update the complex phylogenetic past of baleen whales, because it splits up an otherwise long branch that leads to the radiation of rorquals. (lu.se)
To do so, we constructed a multi-species coalescent tree from fragments of a whole-genome alignment and quantified the amount of introgression in the early evolution of rorquals. (lu.se)

Phylogenetic studies showed that the HCoV-HKU1 nucleoprotein gene was relatively conserved compared to NCBI reference sequences, while the 1ab gene of HCoV-NL63 showed more variation. (hindawi.com)
You can browse and download gene phylogenetic trees and multiple sequence alignments. (elixir-europe.org)
according to morphological, physiological and its 16S rRNA gene sequence. (researchgate.net)
A Collection of Conserved Non-Coding Sequences to Study Gene Regulation in Flowering Plants' (Van de Velde et al. (ugent.be)
Gene segments were cloned and sequenced. (who.int)
Next, the isolates were differentiated by sequencing a specific region of the gene encoding the enzyme glucosyltransferase B ( gtfB ). (bvsalud.org)
Based on the genetic similarity of the isolates and pattern of amino acid variations identified by partial sequencing of the gtfB gene, base-pair changes were identified and correlated with different virulence patterns among the isolates. (bvsalud.org)
Conclusions: The partial sequencing of the gtfB gene can be a useful tool for elucidating the colonization patterns of S. mutans . (bvsalud.org)
In addition, IGS sequencing (e.g., sequencing of intergenic regions between the 16S and 23S rRNA genes) has been used to taxonomy studies, while partial sequencing of the gene gtfB , which encodes the enzyme glucosyltransferase B, has been used to investigate enzymatic activity and virulence 11-12 . (bvsalud.org)

Multiple sequence alignment is typically the first step in estimating phylogenetic trees, with the assumption being that as alignments improve, so will phylogenetic reconstructions. (illinois.edu)

From the resulting MSA, sequence homology can be inferred and phylogenetic analysis can be conducted to assess the sequences' shared evolutionary origins. (wikipedia.org)
In order to do that a novel protein sequence enters into the software along with a list of known protein identifiers chosen by the biologist to perform a homology search, followed by a multiple sequence alignment and finally a phylogenetic analysis. (myexperiment.org)
Phylogenetic tree showed Bmuccr hadhigh homology with T. castaneum homologous. (researchgate.net)
Areas covered include sequence databases, pairwise and multiple sequence alignment, homology searches in sequence databases and subcellular localization prediction. (lu.se)

For nucleotide sequences, a similar gap penalty is used, but a much simpler substitution matrix, wherein only identical matches and mismatches are considered, is typical. (wikipedia.org)

In this paper, we report on a simulation study that we performed to evaluate the consequences of using these new multiple sequence alignment methods in terms of the resultant phylogenetic reconstruction. (illinois.edu)
The Environment for Tree Exploration (ETE) is a computational framework that simplifies the reconstruction, analysis, and visualization of phylogenetic trees and multiple sequence alignments. (nih.gov)
Alignment-Free Phylogenetic Reconstruction: Sample Complexity via a Branching Process Analysis. (mit.edu)

The identification and characterization of macromolecular sequences and their higher-order structures have utilized a very important principle in molecular and evolutionary biology. (biomedcentral.com)
In many cases, the input set of query sequences are assumed to have an evolutionary relationship by which they share a linkage and are descended from a common ancestor. (wikipedia.org)
For proteins, this method usually involves two sets of parameters: a gap penalty and a substitution matrix assigning scores or probabilities to the alignment of each possible pair of amino acids based on the similarity of the amino acids' chemical properties and the evolutionary probability of the mutation. (wikipedia.org)
Evolutionary sequences and phylogenetic trees can be read, viewed, modified and simulated. (haskell.org)
Handle evolutionary sequences and multi sequence alignments. (haskell.org)
Analyze, modify, and simulate evolutionary sequences. (haskell.org)
Phylogenetic analysis revealed the evolutionary relationships between the GA2oxs. (bvsalud.org)

Multiple dimensions of cross-indexed information are contained within the relational database - rCAD, including sequence alignments, the NCBI phylogenetic tree, and comparative secondary structure information for each aligned sequence. (biomedcentral.com)
this was done by exploring existing bacteriocin databases such as BAGEL4, BACTIBASE, Uniprot, NCBI Protein, and also by writing my own Bash scripts to mine antimicrobial databases such as Antismash, where bacteriocin sequences are not so easily available. (bspp.org.uk)

Issue with visualising cladogram/phylogenetic tree with multiple sequence alignment data in R? (stackexchange.com)
I would like to visualize tree with multiple sequence alignment. (stackexchange.com)
Multiple sequence alignment (MSA) may refer to the process or the result of sequence alignment of three or more biological sequences, generally protein, DNA, or RNA. (wikipedia.org)
Multiple sequence alignment is often used to assess sequence conservation of protein domains, tertiary and secondary structures, and even individual amino acids or nucleotides. (wikipedia.org)
Most multiple sequence alignment programs use heuristic methods rather than global optimization because identifying the optimal alignment between more than a few sequences of moderate length is prohibitively computationally expensive. (wikipedia.org)
A general approach when calculating multiple sequence alignments is to use graphs to identify all of the different alignments. (wikipedia.org)
There are various alignment methods used within multiple sequence to maximize scores and correctness of alignments. (wikipedia.org)
We present SeaView version 4, a multiplatform program designed to facilitate multiple alignment and phylogenetic tree building from molecular sequence data through the use of a graphical user interface. (hal.science)
This includes data collection with accurate annotation, structure prediction, multiple sequence-structure alignment and fast tree calculation. (jove.com)
which were further characterised by multiple sequence alignment and phylogenetic analysis. (bspp.org.uk)
The multiple sequence alignment of 16 subunit VII homologues showsthat Bmuccr is very hydrophilic, has a characteristic charge distribution, and has a high helical content. (researchgate.net)
Multiple sequence alignment revealed sequence relatedness between the GA2oxs. (bvsalud.org)

SeaView version 4 combines all the functions of the widely used programs SeaView (in its previous versions) and Phylo_win, and expands them by adding network access to sequence databases, alignment with arbitrary algorithm, maximum-likelihood tree building with PhyML, and display, printing, and copy-to-clipboard of rooted or unrooted, binary or multifurcating phylogenetic trees. (hal.science)
PhyML is a software that estimates maximum likelihood phylogenies from alignments of nucleotide or amino acid sequences. (debian.net)

Forty-nine isolates of Trichoderma from the Brazilian Midwest were evaluated for their antagonistic activity in vitro against Sclerotinia sclerotiorum (causal agent of white mold), which were then identified based on their nuclear ribosomal ITS sequences. (scielo.br)
By sequencing the 16S-23S intergenic region, it was found that all of the isolates belonged to the species S. mutans . (bvsalud.org)

Our Capacity-Building in Genomic Surveillance and Epidemiology program aims to build genomic surveillance using portable and affordable sequencing such as the Oxford Nanopore Technologies MinION platform and bioinformatics and phylodynamics modeling capabilities to enable a more efficient response to disease outbreaks. (nih.gov)
Background: Protein sequence alignment is one of the basic tools in bioinformatics. (sciweavers.org)

This comparative method is now widely used in the study for many RNAs, and is the cornerstone for the computational analysis of the deluge of nucleic acid sequences that are determined with next-generation sequencing methodology. (biomedcentral.com)

To test this, we aligned 97 protein sequences consisting of homologs of UMAMIT clade I from 27 plant species and created sequence logos containing the 51 residues identified in the structural analysis ( Supplementary Figure 1 ). (frontiersin.org)
Two samples were co-infected with HRV-A and HRV-B or HRV-C. By comparative analysis of the VP4/VP2 sequences of the 66 HRVs, we showed a high diversity of strains in HRV-A and HRV-B species, and a prevalence of 51.5% of strains that belonged to the recently identified HRV-C species. (plos.org)
When analyzing a fragment of the 5′ UTR, we characterized at least two subspecies of HRV-C: HRV-Cc, which clustered differently from HRV-A and HRV-B, and HRV-Ca, which resulted from previous recombination in this region with sequences related to HRV-A. The full-length sequence of one strain of each HRV-Ca and HRV-Cc subspecies was obtained for comparative analysis. (plos.org)
The analysis of RNA sequences, once a small niche field for a small collection of scientists whose primary emphasis was the structure and function of a few RNA molecules, has grown most significantly with the realizations that 1) RNA is implicated in many more functions within the cell, and 2) the analysis of ribosomal RNA sequences is revealing more about the microbial ecology within all biological and environmental systems. (biomedcentral.com)
Two computer systems that utilize the Gutell lab's RNA Comparative Analysis Database (rCAD) were developed to align sequences to an existing template alignment available at the Gutell lab's Comparative RNA Web (CRW) Site. (biomedcentral.com)
This workflow performs a generic protein sequence analysis. (myexperiment.org)
Therefore comparative genomic analysis of T . equi was undertaken to: 1) identify genes contributing to immune evasion and persistence in equid hosts, 2) identify genes involved in PBMC infection biology and 3) define the phylogenetic position of T . equi relative to sequenced apicomplexan parasites. (biomedcentral.com)
Comparative genomic analysis of T . equi revealed the phylogenetic positioning relative to seven apicomplexan parasites using deduced amino acid sequences from 150 genes placed it as a sister taxon to Theileria spp . (biomedcentral.com)
Our analysis identified 50 genes that will be useful for definitive phylogenetic classification of T . equi and closely related organisms. (biomedcentral.com)

Different primary structures (or sequences) can form the same higher-order structure for different RNAs and proteins [ 5 ]. (biomedcentral.com)
For example, some changes in DNA sequences do not lead to changes in proteins. (thetech.org)

Visual depictions of the alignment as in the image at right illustrate mutation events such as point mutations (single amino acid or nucleotide changes) that appear as differing characters in a single alignment column, and insertion or deletion mutations (indels or gaps) that appear as hyphens in one or more of the sequences in the alignment. (wikipedia.org)

MSAs require more sophisticated methodologies than pairwise alignment because they are more computationally complex. (wikipedia.org)
For n individual sequences, the naive method requires constructing the n-dimensional equivalent of the matrix formed in standard pairwise sequence alignment. (wikipedia.org)
In 1989, based on Carrillo-Lipman Algorithm, Altschul introduced a practical method that uses pairwise alignments to constrain the n-dimensional search space. (wikipedia.org)
In this approach pairwise dynamic programming alignments are performed on each pair of sequences in the query set, and only the space near the n-dimensional intersection of these alignments is searched for the n-way alignment. (wikipedia.org)

This was confirmed by the high similarity (99.2%-100%) of their sequences with those available in GenBank. (who.int)

The accuracies of the two CRWAlign programs were compared with the best template-based rRNA alignment programs and the best de-novo alignment programs. (biomedcentral.com)
In addition, the use of bacterial 16S rRNA sequencing in the identification of the microbiome in many different environmental systems creates a need for rapid and highly accurate alignment of bacterial 16S rRNA sequences. (biomedcentral.com)

Or it can be built from molecular information, like genetic sequences. (thetech.org)

The accurate and rapid alignment of these RNA sequences is essential to decipher the maximum amount of information from this data. (biomedcentral.com)
If data is a multi sequence alignment, additionally analyze columns. (haskell.org)
All raw and consensus viral sequence data should be deposited in the European Nucleotide Archive (ENA) . (elixir-europe.org)
If you already upload consensus sequence data to GISAID , we encourage you to also upload your data to the ENA. (elixir-europe.org)
We will perform some maintenance operations fixing missing bootstrap values in the phylogenetic trees as well as updating depending data types. (ugent.be)
In practice however, the amount of memory required to process a data set is proportional of the product of the number of sequences by their length. (debian.net)
This hands on course will give you additional experience in analyzing next generation sequencing data. (lu.se)

The Tubingen group has led the development of phylogenetic network algorithms, and this book delivers a clear exposition for biologists bewildered by a plethora of recent methods, as well as for bioinformaticians aiming to develop the field further. (uni-tuebingen.de)
Computational algorithms are used to produce and analyse the MSAs due to the difficulty and intractability of manually processing the sequences given their biologically-relevant length. (wikipedia.org)

The above mentioned code is generating tree with the alignment matrix, but the tree root tip labels are not visible. (stackexchange.com)
One reason for this is the lack of robust and accepted methods for inferring non-tree histories or phylogenetic networks. (uni-tuebingen.de)
More recently, we have focused on developing methods for rooted phylogenetic networks, which we will make available via our tree- and network drawing program Dendroscope. (uni-tuebingen.de)
A phylogenetic tree is a diagram used to show how organisms are related to one another. (thetech.org)
As long as you have something you can compare across different species, you can make a phylogenetic tree. (thetech.org)
A phylogenetic tree can be built using physical information like body shape, bone structure, or behavior. (thetech.org)
Any DNA, RNA, or protein sequence can be used to generate a phylogenetic tree. (thetech.org)
What's in a phylogenetic tree? (thetech.org)
In a phylogenetic tree, each line is called a branch . (thetech.org)
How to construct a phylogenetic tree? (thetech.org)
To construct a tree, we'll compare the DNA sequences of different species. (thetech.org)
The main strengths of PhyML lies in the large number of substitution models coupled to various options to search the space of phylogenetic tree topologies, going from very fast and efficient methods to slower but generally more accurate approaches. (debian.net)

The present study investigated the response of A. simplex (s. s.) third stage larvae (identified to species level by mtDNA cox2 sequencing) to the storage time a. (researchgate.net)
But as species evolve and diverge, they will accumulate changes in the DNA sequences. (thetech.org)
The 16S rDNA sequencing of lyophilized treated sample was carried out to correlate the phylogenetic relationship of P. vulgaris with other bacterial species after treatment. (slideserve.com)
ABSTRACT A diagnostic polymerase chain reaction (PCR) assay using species-specific primers and direct sequencing was used to identify members of the Anopheles maculipennis complex in the north-west and central regions of the Islamic Republic of Iran. (who.int)

How do scientists construct phylogenetic trees and know the degree of relatedness between living organisms by DNA? (thetech.org)

Each of the graph edges has a weight based on a certain heuristic that helps to score each alignment or subset of the original graph. (wikipedia.org)

We cloned and sequenced a 924-nt fragment that covered part of the 5′UTR and the VP4/VP2 capsid genes. (plos.org)

The second program, CRWAlign-2 creates a profile based on phylogenetic, secondary structure, and sequence information. (biomedcentral.com)
The ITS2 Database is a workbench for phylogenetic inference simultaneously considering sequence and secondary structure of the internal transcribed spacer 2. (jove.com)

We find that while alignment accuracy is positively correlated with phylogenetic accuracy, the amount of improvement in phylogenetic estimation that results from an improved alignment can range from quite small to substantial. (illinois.edu)

The taxon known as C. apodocarpa is well supported by likelihood- and parsimony-based molecular phylogenetic inferences as well as morphology, chemistry, and ecology. (datadryad.org)

Methods: S. mutans samples were isolated from the saliva of 30 children with varying histories of dental caries, and they were characterized according to morphological and biochemical markers and the sequences of their 16S-23S intergenic spacer region. (bvsalud.org)

This textbook, by one of the leaders of the field (Daniel Huson) and his co-authors, provides a mathematically rigorous introduction to one of the most exciting and beautiful research areas in computational biology: phylogenetic networks. (uni-tuebingen.de)

A direct method for producing an MSA uses the dynamic programming technique to identify the globally optimal alignment solution. (wikipedia.org)

CoV-AbDab: the Coronavirus Antibody Database is a database of coronavirus-binding antibody sequences and structures. (elixir-europe.org)

Out of 20 positive samples, 13 (65%) gave satisfactory sequencing results. (lww.com)

The scores in the substitution matrix may be either all positive or a mix of positive and negative in the case of a global alignment, but must be both positive and negative, in the case of a local alignment. (wikipedia.org)

You can actually calculate how similar any two sequences are, and make a table to compare all the differences. (thetech.org)

We observe that phylogenetic accuracy is most highly correlated with alignment accuracy when sequences are most difficult to align, and that variation in alignment accuracy can have little impact on phylogenetic accuracy when alignment error rates are generally low. (illinois.edu)
With most standard personal computers, the "comfort zone" for PhyML generally lies around 3 to 500 sequences less than 2,000 character long. (debian.net)

Moreover, Next-generation sequencing (NGS) technologies provide a rapid, precise method for generating HDV genomes to define infecting genotypes. (researchsquare.com)
To look for bacteriocin sequences in the genomes, I ran a protein alignment tool called Diamond, using our annotated genomes and the bacteriocin database as input. (bspp.org.uk)

Our work in this area was originally focused on developing methods for inferring unrooted phylogenetic networks and our computer program, SplitsTree, is currently the most widely-used software for the construction of phylogenetic networks. (uni-tuebingen.de)
Phylogenetic Networks provides a long-overdue exposition of network-based methods, their possible uses, and details on practical software. (uni-tuebingen.de)

With the advancement of next-generation sequencing and mass spectrometry, there is a growing need for the ability to merge biological features in order to study a system as a whole. (rsc.org)

Anatomy4

Organisms13

Diseases1

Chemicals and Drugs32

Analytical, Diagnostic and Therapeutic Techniques and Equipment39

Psychiatry and Psychology1

Phenomena and Processes70

Disciplines and Occupations3

Anthropology, Education, Sociology and Social Phenomena1

Technology, Industry, Agriculture4

Information Science39

Health Care15

Analyses12

Genome11

Gene9

Estimating phylogenetic trees1

Homology4

Nucleotide sequences1

Reconstruction3

Evolutionary7

NCBI2

Multiple12

Maximum-likelihood2

Isolates2

Bioinformatics2

Nucleic acid1

Analysis9

Proteins2

Amino1

Pairwise4

Similarity1

RRNA2

Genetic1

Data7

Algorithms2

Tree12

Species4

Relatedness1

Heuristic1

Genes1

Secondary2

Estimation1

Morphology1

Morphological1

Computational1

Optimal alignment1

Structures1

Results1

Matrix1

Calculate1

Generally2

Genomes2

Methods2

Biological1