Alignment sequence. Medical search. Frequent questions

MSA refers to the alignment of three or more biological sequences, protein or nucleic acid of similar length. (projectguru.in)
These methods are identical to ones used for previous work with amplicon and native nucleic acid sequencing ( 2 - 6 ). (cdc.gov)

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)
The first and most important step in studying a newly discovered protein sequence is to search protein databases for proteins that are similar or closely-related to the new protein, and then to align the new protein sequence to these proteins. (concordia.ca)
A common starting point for the computational analysis of proteins is the construction of a multiple sequence alignment (MSA). (blogspot.com)
It also determines the consensus sequence of the aligned sequences and reveals biological facts about proteins. (projectguru.in)
For example, some changes in DNA sequences do not lead to changes in proteins. (thetech.org)
A ACACTAFKL Dayhoff and her team used sequences that were at least 85% similar and calculated the frequency with which each protein was substituted for each of the other proteins. (slidetodoc.com)

Analisis pada data genetik protein dapat dilakukan dengan melakukan penyejajaran sekuen ( sequence alignment) yaitu proses menyejajarkan suatu sekuen dengan satu atau beberapa sekuen lain sehingga diperoleh tingkat kesamaan di antaranya ( sequence similarity ). (polibatam.ac.id)
The 1 means that given the degree of similarity between the sequences used to make up the matrix, the scores in this matrix are the frequencies for one evolutionary time unit. (slidetodoc.com)
Random similarity of sequences or sequence sections can impede phylogenetic analyses or the identification of gene homologies. (leibniz-lib.de)
It is therefore important to identify possible random similarity within sequence alignments in advance of model estimation and tree reconstructions. (leibniz-lib.de)
We propose an alternative method which can identify random similarity within multiple sequence alignments based on Monte Carlo resampling within a sliding window. (leibniz-lib.de)
The method infers similarity profiles from pairwise sequence comparisons and subsequently calculates a consensus profile. (leibniz-lib.de)
In consequence, consensus profiles identify dominating patterns of non-random similarity or randomness within sections of multiple sequence alignments. (leibniz-lib.de)
BLAST (Basic Local Alignment Search Tool) finds regions of similarity between biological sequences. (addgene.org)
This was confirmed by the high similarity (99.2%-100%) of their sequences with those available in GenBank. (who.int)
There are four plots to indicate similarity in the alignment positions plus two plots, those fro hydropathy and polarity, to show trends in amino acid propensities. (lu.se)

Amino acid or nucleotide sequence. (mathworks.com)
To deselect, click back on the nucleotide sequence. (addgene.org)
Displays a graphical map based on nucleotide sequence data labeled with restriction enzymes, plasmid features, ORFs (theoretical open reading frames) and primers. (addgene.org)
List of restriction enzymes that can cut a given nucleotide sequence. (addgene.org)
List of common features detected in a given nucleotide sequence. (addgene.org)

The defining feature of the protein-alignment-guided assembly is that it uses existing protein alignments to detect DNA overlaps between reads. (biomedcentral.com)
At this point GISMO works only for protein alignments and the authors are the first to point out that there is room for improvement. (blogspot.com)

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)
This program switches between different alignment algorithms and between sequences and profiles, so I wanted to create a library that aligns any collection of objects with various algorithms using the same syntax. (github.com)
Details of the algorithms used in Opal are available in the original ISMB paper, which should be cited in the event Opal is used: Wheeler, T.J. and Kececioglu, J.D. Multiple alignment by aligning alignments, Proceedings of the 15th ISCB Conference on Intelligent Systems for Molecular Biology (ISMB), Bioinformatics 23, i559-i568, 2007. (arizona.edu)
In spite of considerable research and efforts that have been recently deployed for improving the performance of multiple sequence alignment (MSA) algorithms, finding a highly accurate alignment between multiple protein sequences still remains a challenging problem. (concordia.ca)
Bioinformatics program for analysing two (currently) or more (in the future) protein sequences and compare them using a Smith-Waterman and/or Needleman-Wunsch algorithms. (over-update.download)
The third is necessary because algorithms for both multiple sequence alignment and structural alignment use heuristics which do not always perform perfectly. (over-update.download)
The 'msa' package provides a unified R/Bioconductor interface to the multiple sequence alignment algorithms ClustalW, ClustalOmega, and Muscle. (bioconductor.org)
The multiple sequence alignment algorithms are complemented by a function for pretty-printing multiple sequence alignments using the LaTeX package TeXshade. (bioconductor.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)
There are various alignment methods used within multiple sequence to maximize scores and correctness of alignments. (wikipedia.org)
History: Alignlib contains a collection of methods for classical biological sequence alignment. (github.com)
GSNAP uses highly efficient methods for reference- based alignment by compressing the reference sequence. (genecodes.com)
Multiple Sequence Alignment (MSA) methods are typically benchmarked on sets of reference alignments. (vu.nl)
Using this new score along with the standard SP score, we investigate the discriminatory behavior of the new score by assessing how well six different MSA methods perform with respect to BAliBASE reference alignments. (vu.nl)
However, for more divergent reference alignments the SPdist score is able to distinguish between methods that keep alignments approximately close to the reference and those exhibiting larger shifts. (vu.nl)
We observed that by using SPdist together with SP scoring we were able to better delineate the alignment quality difference between alternative MSA methods. (vu.nl)
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 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)
At least under moderate conditions, the approximate methods can quite accurately calculate ab initio alignment probabilities under biologically more realistic models than before. (biomedcentral.com)
Since the groundbreaking works by Bishop and Thompson [ 13 ] and by Thorne, Kishino and Felsenstein [ 14 ], many studies have been done to develop and apply methods to calculate the probabilities of pairwise alignments (PWAs) and multiple sequence alignments (MSAs) under the probabilistic models aiming to incorporate the effects of indels. (biomedcentral.com)
Observer agreement for event sequences: Methods and software for sequence alignment and reliability estimates. (bvsalud.org)
Tissue samples will be collected from mammalian species, ranging from rodents to non-human primates (NHPs), and subjected to various sequencing methods, including bulk sequencing of tissue samples, 10X single nuclei sequencing, and Parse Bio single nuclei sequencing. (lu.se)
In this project, we use principles from multidimensional solid-state NMR spectroscopy to design new MRI pulse sequences and data processing methods for investigating cell density, shape, alignment, heterogeneity, and membrane permeability. (lu.se)

Align homologous protein sequences and structures. (simtk.org)
1996 for mercury phytoremediation, with respect to its homologous protein sequences. (projectguru.in)

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)
Opal is software for aligning multiple biological sequences. (arizona.edu)

Read alignment maps short DNA sequences to a reference genome to discover conserved and polymorphic regions of the genome. (umd.edu)
Read Mapping: alignment of reads to a specified reference genome (human, mouse or rat). (lu.se)

CLUSTAL 2.1 Multiple Sequence Alignments DATA (sequences) -INFILE=file.ext :input sequences. (github.io)
CLUSTAL 2.1 Multiple Sequence Alignments [1] "Multiple Alignment successfully written in /var/folders/tb/ v6lh8_g505bfjytt3lvdmvw00000gn/T//RtmpOXdtWL/_alignment/multi_aln/clustalw.aln. (github.io)
Group 1: Delayed Alignment Score 29 CLUSTAL-Alignment file created [/var/folders/tb/v6lh8_g505bfjytt3lvdmvw00000gn/T//RtmpOXdtWL/_alignment/multi_aln/clustalw.aln] [1] "Multiple Alignment successfully written in /var/folders/tb/v6lh8_g505bfjytt3lvdmvw00000gn/T//RtmpOXdtWL/_alignment/multi_aln/clustalw.aln. (github.io)
MultiDisp accepts alignments in Clustal, FASTA, MUSCLE, PROBCONS and and Stockholm (Pfam) file format. (lu.se)

Details of this approach are available in the following paper, which should be cited if secondary-structure-based alignment is performed: Kim, E., Wheeler, T.J., and Kececioglu, J.D. Learning models for aligning protein sequence with predicted secondary structure, Proceedings of the 13th Conference on Research in Computational Molecular Biology (RECOMB), Springer-Verlag Lecture Notes in Bioinformatics 5541: 586-605, 2009. (arizona.edu)
Thus, the alignment of multiple protein sequences is one of the most commonly performed tasks in bioinformatics analyses, and has been used in many applications, including sequence annotation, phylogenetic tree estimation, evolutionary analysis, secondary structure prediction and protein database search. (concordia.ca)

MSAs require more sophisticated methodologies than pairwise alignment because they are more computationally complex. (wikipedia.org)
First, for each of all types of local pairwise alignments (PWAs) and some typical types of local multiple sequence alignments (MSAs), we numerically computed the total contribution from all parsimonious indel histories and that from all next-parsimonious histories, and compared them. (biomedcentral.com)
Then we compared the first-approximate probability of each local MSA with its absolute frequency in the MSAs created via a genuine sequence evolution simulator, Dawg. (biomedcentral.com)
MultiDisp is a tool for analysing and visualising multiple sequence alignments (MSAs). (lu.se)

abstract = "Splicing is a biological phenomenon that removes the non-coding sequence from the transcripts to produce a mature transcript suitable for translation. (edu.au)
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)

In this article, the protein sequence of merA enzyme is studied with respect to its closely related sequences found in NCBI database, through Multiple Sequence Alignment (MSA) . (projectguru.in)

This approach is not only faster, but is also better at finding biologically relevant signals within such alignments. (blogspot.com)

To study this phenomenon, information on the intron-exon arrangement of a gene is essential, usually obtained by aligning mRNA/EST sequences to their cognate genomic sequences. (edu.au)
This is facilitated by directing primer and probe design to evolutionarily conserved regions identified through multiple sequence alignments that portray geographical and temporal genomic variability. (nature.com)

Microbiome sequencing projects typically collect tens of millions of short reads per sample. (biomedcentral.com)
Indeed most commonly used alignment tools typically compare sequences and rank alternatives at each branching step based on available information to decide which branch to follow. (blogspot.com)
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)

Swift is a DNA sequence alignment program that produces gapped alignment using the Smith-Waterman algorithm. (over-update.download)
Pada makalah ini dibahas bagaimana melakukan sequence alignment pada sekuen protein menggunakan algoritma Smith-Waterman secara terkomputerisari, serta menentukan nilai konstanta yang digunakan untuk kesamaan dan ketidaksamaan residu. (polibatam.ac.id)

The Mauve alignment method is not supported in this workflow. (dnastar.com)

The Sequence Alignment/Map (SAM) format is a generic alignment format for storing read alignments against reference sequences, supporting short and long reads (up to 128 Mbp) produced by different sequencing platforms. (nih.gov)
BWA-MEM is designed to align sequence reads ranging from 70bp to 1Mbp to a reference. (genecodes.com)
(1) Heng Li Aligning sequence reads, clone sequences and assembly contigs with BWA-MEM 2013 arXiv:1303.3997v2 [q-bio.GN] Please note that this reference is a preprint hosted at arXiv.org . (genecodes.com)
Depending on the goals of the project, the short reads can either be subjected to direct sequence analysis or be assembled into longer contigs. (biomedcentral.com)
The assembly of whole genomes from metagenomic sequencing reads is a very difficult problem. (biomedcentral.com)
Genes are assembled on the fly, based on the alignment of all reads against a protein reference database such as NCBI-nr. (biomedcentral.com)
Using published synthetic community metagenome sequencing reads and a set of 41 gene families, we show that the performance of this approach compares favorably with that of full-featured assemblers and that of a recently published HMM-based gene-centric assembler, both in terms of the number of reference genes detected and of the percentage of reference sequence covered. (biomedcentral.com)
Sequencing is performed on NovaSeq 6000, with read structure of 2 x 150 bp and aiming for 25M reads per sample. (lu.se)

To provide a fresh and less-biased global set of analyses, large-scale comparative DNA sequence alignments between the chimpanzee and human genomes were performed with the BLASTN algorithm. (icr.org)
This is significant since the magnitude of alignment shifts is often of relevance in biological analyses, including homology modeling and MSA refinement/manual alignment editing. (vu.nl)
First, it is indels but not substitutions that yield the skeletons (or the gap configurations) of the sequence alignments (reviewed, e.g., in [ 7 ]), which provide essential inputs to most homology-based analyses in computational biology. (biomedcentral.com)
Afin de remédier à ce problème et d'étudier les variations génétiques et antigéniques des virus A(H1N1)pdm09 et H3N2, nous avons procédé à des analyses génétiques et phylogénétiques des gènes de l'hémagglutinine (HA) et de la neuraminidase (NA) de ces virus, sur la période 2011-2013 en Jordanie. (who.int)

It is flexible in style, compact in size, efficient in random access and is the format in which alignments from the 1000 Genomes Project are released. (nih.gov)
6,635 total entires, with the 2 stock genomes added from this study) and top hits and alignment statistics were generated. (cdc.gov)

While BESTFIT's randomize is rather crude I should recommend W.Pearson's RDF2 which also permits to suffle *windows* of the sequence, thus leaving the sequence more intact than the pure monte carlo would permit. (bio.net)

Insertions and deletions (indels) account for more nucleotide differences between two related DNA sequences than substitutions do, and thus it is imperative to develop a method to reliably calculate the occurrence probabilities of sequence alignments via evolutionary processes on an entire sequence. (biomedcentral.com)
Previously, we presented a perturbative formulation that facilitates the ab initio calculation of alignment probabilities under a continuous-time Markov model, which describes the stochastic evolution of an entire sequence via indels with quite general rate parameters. (biomedcentral.com)
Here, using our formulation, we attempt to approximately calculate the probabilities of local alignments under space-homogeneous cases. (biomedcentral.com)

Why do recent versions generate LONG alignments? (cbrc.jp)
Returns only the alignments used to generate the HMM profile. (mathworks.com)
Any DNA, RNA, or protein sequence can be used to generate a phylogenetic tree. (thetech.org)

From the resulting MSA, sequence homology can be inferred and phylogenetic analysis can be conducted to assess the sequences' shared evolutionary origins. (wikipedia.org)
The chimp sequences were subsequently implicated by personal correspondence with NCBI staff and supporting data from this study to be pre-screened for some level of homology to the human genome. (icr.org)
Areas covered include sequence databases, pairwise and multiple sequence alignment, homology searches in sequence databases and subcellular localization prediction. (lu.se)

To assess how well individual gene sequences are assembled , we report the percentage of sequence covered by the longest contig that maps to a given reference sequence. (biomedcentral.com)
To assess how well gene sequences are detected for different organisms, we report the number of organisms for which the longest mapped contig covers at least half of the corresponding reference sequence. (biomedcentral.com)
In our evaluation, we find that the MEGAN assembler performs best in terms of the percentage of reference genes covered and percentage of reference gene sequences detected. (biomedcentral.com)
In the previous article , similar gene sequences of an established mercuric ion reductase or merA gene were identified. (projectguru.in)

package provides multiple functions to perform pairwise and multiple sequence alignments. (github.io)

MGAlign is a novel, rapid, memory efficient and practical method for aligning mRNA/EST and genome sequences. (edu.au)
FSA is a probabilistic multiple sequence alignment algorithm which uses a 'distance-based' approach to aligning homologous protein, RNA or DNA FSA is a probabilistic multiple sequence alignment algorithm which uses a 'distance-based' approach to aligning homologous protein, RNA or DNA sequences. (over-update.download)
PACid_16033839 245 aa Start of Pairwise alignments Aligning. (github.io)
Score: 2 Guide tree file created: [/Library/Frameworks/R.framework/Versions/3.1/Resources/library/orthologr/seqs/aa_seqs.dnd] There are 1 groups Start of Multiple Alignment Aligning. (github.io)

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)
Through the study undertaken in this thesis it is shown that a reliable detection of indels and their flanking regions can be achieved by using the proposed IndelFR predictors, and a substantial improvement in the protein alignment accuracy can be achieved by using the proposed variable gap penalty function. (concordia.ca)

These data are used for a wide variety of important biological analyzes, including genome sequencing, comparative genomics, transcriptome analysis, and personalized medicine but are complicated by the volume and complexity of the data involved. (umd.edu)
GSNAP is designed to preform reference-based alignment of Illumina-Solexa or Sanger standard data that is both paired-ended and unpaired-ended. (genecodes.com)
Length of the sequence is not an issue with GSNAP because it has the ability to align very short to arbitrarily long data lengths with ease. (genecodes.com)
The popular Maq algorithm aligns single-end and paired-end Next-Generation data to a reference sequence. (genecodes.com)
Individual BLASTN query jobs each involved a data set of 40,000 chimpanzee whole genome shotgun sequences (WGSS) obtained from the National Center for Biotechnology (NCBI) and queried against four different human genome assemblies (GRCH37, GRCH36, Alternate SNP Assembly, and the Celera Assembly). (icr.org)
This data includes three Figures that are showing the sequence alignment analysis on human Dicer. (mendeley.com)
They then built phylogenetic trees where each transition from generation to generation has as few changes as possible, given the data, in each ancestral sequence. (slidetodoc.com)
The approach has been extended to aminoacid and nucleotide data and is currently further developed to visualize total randomness among sequences of a multiple sequence alignment together with Dr. Patrick Kück and Sandra Meid, both ZFMK. (leibniz-lib.de)
Use with SnapGene software or the free Viewer to visualize additional data and align other sequences. (addgene.org)
The wizard is started after successfully demultiplexing and merging data from a sequencing run. (lu.se)
This hands on course will give you additional experience in analyzing next generation sequencing data. (lu.se)
Data from COVID-19 case investigations, contact tracing, the Commonwealth's immunization registry and whole genome sequencing were collated and analysed as part of this study. (who.int)
After sequencing, data will be kept by CTG for 3 months and subsequently deleted . (lu.se)
Demultiplexed data files generated from the Illumina sequencing run. (lu.se)
Pipeline Development: The bioinformatic pipeline will be developed to process and analyze the sequencing data generated from the experimental part of the project. (lu.se)

You can also use '-' and '/' characters in this sequence to add gaps and chain breaks. (salilab.org)
In contrast to the " Profile alignment " method, this method retains existing gaps, and adds new gaps, if necessary. (dnastar.com)

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)

Besides the alignment itself, this web service allows users to effectively visualize the alignment in a graphical manner and to perform limited analysis on the alignment output. (edu.au)

We conducted a phylogenetic analysis of the section, including samples of all species, using sequences of the ITS and ETS regions of nuclear ribosomal DNA. (bioone.org)
To construct a tree, we'll compare the DNA sequences of different species. (thetech.org)
But as species evolve and diverge, they will accumulate changes in the DNA sequences. (thetech.org)
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)

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)
As new protein sequences are discovered on an everyday basis and protein databases continue to grow exponentially with time, analysis of protein families, understanding their evolutionary trends and detection of remote homologues have become extremely important. (concordia.ca)

Two fundamental computations in computational biology are read alignment and genome assembly. (umd.edu)
Genome assembly computes the sequence of a genome from many short DNA sequences. (umd.edu)
If you want to learn more about Next-Generation Assembly, check out the Next-Generation Sequence Alignment and Advanced Next-Generation Sequence Alignment Tutorials. (genecodes.com)
We present a new method for performing gene-centric assembly, called protein-alignment-guided assembly, and provide an implementation in our metagenome analysis tool MEGAN. (biomedcentral.com)
Protein-alignment-guided assembly of orthologous gene families complements whole-metagenome assembly in a new and very useful way. (biomedcentral.com)
In this paper, we present a new approach to gene-centric assembly that we call protein-alignment-guided assembly . (biomedcentral.com)
The main technical contribution of this paper is the design and implementation of a "protein-alignment-guided" assembly algorithm that is explicitly designed for gene-centric assembly. (biomedcentral.com)
Assembly of the alignments into full transcripts and quantification of the expression levels of each gene/transcript. (lu.se)
The key reform here will be the alignment of the governing bodies' resolutions with corporate priorities, ensuring a more strategic and disciplined approach to decision-making by the Health Assembly, and enabling the necessary oversight of programme and financial implementation, including the fiscal soundness of Organizational practices. (who.int)

The average chimp query sequence length was 740 bases and depending on the BLASTN parameter combination, average alignment length varied between 121 and 191 bases. (icr.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)
Insertion/deletion (indel) and substitution of an amino acid are two common events that lead to the evolution of and variations in protein sequences. (concordia.ca)
Both the SP and CS scores treat mismatches between a query and reference alignment as equally bad, and do not take the separation into account between two amino acids in the query alignment, that should have been matched according to the reference alignment. (vu.nl)
Maps are used to visualise physicochemical properties of amino acids in the alignment positions. (lu.se)

Add sequences to the project and align some or all of them . (dnastar.com)
It can align both protein and DNA sequences, and expects inputs to be in fasta format. (arizona.edu)
Load an example sequence and align it to the profile structure using the HMM alignment. (mathworks.com)
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)
ALIGN :do full multiple alignment. (github.io)
The first thing to do is align the two DNA sequences together that you're going to compare. (thetech.org)
You can align and compare as many sequences as you want. (thetech.org)
Using 14 C in the marine Cariaco Basin and 10 Be preserved in Greenland ice, the kauri 14 C sequence allows us to precisely align sequences across. (lu.se)
C sequence allows us to precisely align sequences across this period. (lu.se)

The server also permits the alignment to be saved in several forms, both graphical and text, suitable for further processing and analysis by other programs. (edu.au)
UGENE is a comprehensive genome analysis suite that features multiple sequence alignment and a complex HMM builder and search module. (over-update.download)
PFAAT is a Java-based multiple sequence alignment editor and viewer designed for protein family analysis. (over-update.download)
A set of programs for multiple sequence alignment and analysis. (over-update.download)
ALTER focuses on the specifications of mainstream alignment and analysis programs rather than on the conversion among more or less specific. (over-update.download)
The fourth is a great example of how interactive graphical tools enable a worker involved in sequence analysis to conveniently execute a variety if different computational tools to explore. (over-update.download)
Primary sequence alignment analysis of the DUF283 domain was performed based on Arabidopsis DUF283. (mendeley.com)
HA and NA sequences each in the analysis. (who.int)

And we demonstrated that, under some conditions, the ab initio probability of an alignment can be factorized into the product of an overall factor and contributions from regions (or local alignments) delimited by gapless columns. (biomedcentral.com)
These circumstances make it imperative to develop a stochastic model that enables us to reliably calculate the probability of sequence evolution via mutations including insertions and deletions. (biomedcentral.com)
On the meaning, mapQ is nearly the same as baseQ - the phred scaled probability of the alignment/base being wrong. (stackexchange.com)

The objectives of this thesis are to develop a novel scheme to predict indel flanking regions (IndelFRs) in a protein sequence and to develop an efficient algorithm for the alignment of multiple protein sequences incorporating the information on the predicted IndelFRs. (concordia.ca)
In the second part of the thesis, a novel and efficient algorithm incorporating the information on the predicted IndelFRs for the alignment of multiple protein sequences is proposed. (concordia.ca)

Our RNA service includes mRNA and total RNA library preparation and sequencing on Illumina platforms. (lu.se)

Sequoia is a command-line tool for the alignment of molecular protein sequences and atomic structures. (simtk.org)
Or it can be built from molecular information, like genetic sequences. (thetech.org)

Ultra-degenerate primers with 3' termini overlapping the probe-binding site adapt the target through site-directed mutagenesis during qPCR to replace DRM-proximal sequence variation. (nature.com)
Displays both strands of base paired nucleotide sequences with annotated enzymes, plasmid features, ORFs (theoretical open reading frames) and primers. (addgene.org)

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)

Aligners spend a proportion of their time indexing the reference sequence to speed up the overall alignment. (genecodes.com)
The reason that the logarithm is used in the scoring formula is that it allows us, among other things, to add the scores of the aligned residues when we compute the score for an overall alignment of two sequences. (slidetodoc.com)

Sequence divergence within oligonucleotide-binding sites creates primer-template duplex instability and lowers T m . (nature.com)
Insofar as they result from protein functional similarities and differences, the patterns of residue conservation and divergence within such an alignment provide clues to biological function. (blogspot.com)

But DNA sequences are most commonly used in generating trees today. (thetech.org)

Hirschberg's Alignment Algorithm Implementation. (stackexchange.com)
Multiple target alignment is not supported in this implementation. (mathworks.com)

Anatomy19

Organisms15

Diseases16

Chemicals and Drugs25

Analytical, Diagnostic and Therapeutic Techniques and Equipment65

Psychiatry and Psychology2

Phenomena and Processes85

Disciplines and Occupations5

Technology, Industry, Agriculture5

Information Science41

Health Care19

Nucleic acid2

Proteins6

Similarity10

Nucleotide sequence5

Protein alignments2

Algorithms8

Methods15

Homologous protein sequences2

Biological sequences2

Reference genome2

CLUSTAL4

Bioinformatics2

MSAs4

Abstract2

Closely related sequences1

Biologically-relevant1

Genomic2

Typically3

Smith-Waterman2

Workflow1

Reads8

Analyses4

Genomes2

Monte carlo1

Probabilities3

Generate3

Homology3

Gene sequences4

Pairwise and multiple1

Aligning4

Indels2

Data15

Gaps2

Comparative2

Visualize1

Species4

Evolutionary2

Assembly9

BLASTN1

Amino4

Align9

Analysis8

Probability3

Multiple protein2

Platforms1

Molecular2

Primers2

Local alignment1

Overall alignment2

Divergence2

Commonly1

Implementation2