Reads sequence alignment. Medical search. Frequent questions

Target enrichment, coupled with next generation sequencing (NGS), enables high-throughput, deep sequencing of genomic regions of interest. (neb.com)
This technique enables the sequencing of all RNA molecules in a high-throughput manner. (biomedcentral.com)
I'm just thinking out loud about how to incorporate high throughput transcriptome sequencing data into BASE. (lu.se)
Together, with another platform known as LIMS Lite , the ED3N platform will be built out to provide an end-to-end, standardized nationwide process for data transfer, high-throughput workflow integration, genomic reference alignment, variant identification, and collaborative variant interpretation among newborn screening programs. (cdc.gov)

The assembly of whole genomes from metagenomic sequencing reads is a very difficult problem. (biomedcentral.com)
The 1000 genomes project recalibrated their FASTQ files using prior alignment information to improve the data quality. (seqanswers.com)
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)
In several long-read datasets, including healthy and cancerous human genomes, we discovered thousands of novel variants and categorized systematic errors in short-read approaches. (deepdyve.com)
Abstract: Advances in DNA sequencing mean databases of thousands of human genomes will soon be commonplace. (lirmm.fr)
Highly accurate long-read HiFi sequencing data for five complex genomes. (crossref.org)
Nanopore sequencing and the Shasta toolkit enable efficient de novo assembly of eleven human genomes. (crossref.org)
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)

Whole genome sequencing data of 1110 Mycobacterium tuberculosis isolates identifies insertions and deletions associated with drug resistance. (cdc.gov)
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 sequencing (WGS) is a high-resolution typing method that can help foodborne disease investigators distinguish outbreak cases from non-outbreak cases. (who.int)

Next-generation sequencing enables use of whole-ge- interest. (cdc.gov)
Genotyping of microorganisms typically relies on com- Next-generation sequencing technology (next gen) parison of genomic features (e.g., fragment size, re- provides rapid, relatively cost-effective whole-genome se- peats, single-nucleotide polymorphisms [SNPs]) between quence typing (WGST). (cdc.gov)
This kit contains the oligonucleotides, beads, enzymes and buffers required to convert the desired fragments into a sequence-ready library for next-generation sequencing on the Illumina platform and is designed for PE75 or PE150 sequencing. (neb.com)
Prior to the development of massively parallel sequencing (also known as next-generation sequencing ), the only cost-effective way to test more than one gene was serial single-gene testing (i.e., complete testing of one gene that might account for the phenotype before proceeding to testing of the next gene) ‒ an expensive and time-consuming approach with a potentially low yield. (nih.gov)
Next Generation Sequencing (NGS) methods are rapidly providing remarkable advances in our ability to study the molecular profiles of human cancers. (biomedcentral.com)
Next generation sequencing (NGS) is a new frontier in cancer and biomedical research, and these approaches are rapidly becoming the preferred method for human disease-based analysis due to vastly improved genome coverage and resolution [ 1 ]. (biomedcentral.com)
To assess the performance of this new methodology, we performed a comprehensive comparison of AmpliSeq with RNA-seq using two well-established next-generation sequencing platforms (Illumina HiSeq and Ion Torrent Proton). (biomedcentral.com)

We begin with an introduction to bioinformatics and omics data analysis, and conclude with the walkthrough of a simple bioinformatics workflow for aligning transcriptomic sequences with genomic data. (r-bloggers.com)
Through a funding opportunity from CDC's Office of Genomics and Precision Public Health in collaboration with the Office of Advanced Molecular Detection , CDC's Newborn Screening and Molecular Biology Branch will conduct a two-year project to develop a streamlined national newborn screening (NBS) bioinformatics pipeline to help in expanding the use and utility of gene and genomic sequencing in NBS programs. (cdc.gov)
Because state programs screen nearly all babies born in the United States each year, this project's coordinated efforts in expansion and use of sequencing technology and bioinformatics capabilities will have far-reaching implications for equitable delivery of genetics-related information to those at risk across the nation. (cdc.gov)

The defining feature of the protein-alignment-guided assembly is that it uses existing protein alignments to detect DNA overlaps between reads. (biomedcentral.com)

The program reads NBRF/PIR, Pearson (Fasta), EMBL/SwissProt, Intelligenetics and CLUSTAL data formats and has interface and the main functions similar to popular text editor Word. (bio.net)
LABEL accepts files in fasta format, whether multi-line or single line and for any number of sequences. (cdc.gov)
The input FASTA sequence is annotated with predictions--using the form "{PRED:clade}" - while a second file accepting the predicted annotations as fact is also created. (cdc.gov)
MultiDisp accepts alignments in Clustal, FASTA, MUSCLE, PROBCONS and and Stockholm (Pfam) file format. (lu.se)

HiCanu: accurate assembly of segmental duplications, satellites, and allelic variants from high-fidelity long reads. (crossref.org)
PG2 integrates genome and transcriptome sequencing to incorporate protein variants containing amino acid substitutions, insertions, and deletions, as well as non-canonical reading frames, exons, and other variants caused by genomic and transcriptomic variation. (biorxiv.org)
However, recent studies in many organisms and in humans have revealed significant protein sequence variation due to the presence of somatically acquired genetic variants, alternative transcription, and mRNA splicing, which are not necessarily annotated in reference databases. (biorxiv.org)

We demonstrate that TdT-dNTP conjugates can quantitatively extend a primer by a single nucleotide in 10-20 s, and that the scheme can be iterated to write a defined sequence. (nature.com)
What I ended up doing was to choose the read coverage for the lowest covered nucleotide in each codon as each residue's read coverage. (stackexchange.com)
Sequence type: protein or nucleotide *Sequence type: protein or nucleotide **Alignment type: local or global *Sequence type: protein or nucleotide. (wikipedia.org)
Alignment type: local or global *Sequence type: protein or nucleotide *Sequence type: protein or nucleotide Please see List of alignment visualization software. (wikipedia.org)
The use of low complexity sequence masking had the effect of decreasing computational time about 5-6 fold, lengthening the alignments slightly, lowering the number of database hits, and lowering the percent nucleotide identity slightly. (icr.org)
To prepare the sequencing libraries, the ChIP DNA fragments were repaired to generate blunt ends, with a single A nucleotide adding to each end. (nih.gov)
Alignment: Sequencing reads were mapped to the mouse genome (mm8 assembly) using the program Efficient Local Alignment of Nucleotide Data (ELAND) or Bowtie. (nih.gov)
The overall nucleotide sequences between Bat Rp-coronavirus/Shaanxi2011 and Bat Cp-coronavirus/Yunnan2011 indicated 88.7% nt identity. (cdc.gov)
Some of the visualisations are only for protein sequences while others work also for nucleotide sequences. (lu.se)

Sequence similarity, alignment and k-mer algorithms. (aber.ac.uk)
Manual alignment and sequence analysis are facilitated by using group operations and amino acid color-coding reflecting amino acid similarity in physico-chemical and mutational properties, secondary structure propensities, etc. (bio.net)
Partly because bestrophin channels have no sequence or structural similarity to other ion channels, the molecular mechanisms underlying gating are unknown. (elifesciences.org)
Sequence similarity-based taxonomic assignments were conducted as described ( 7 ). (cdc.gov)
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)

Abstract: In this talk, we will begin by illustrating how we integrated hashing and indexing in building an aligner (the ERNE aligner) used to map short patterns (reads) on a long text (reference) with a limited amount of errors. (lirmm.fr)
Abstract: We present the q-group index, a novel data structure for read mapping tailored towards graphics processing units (GPUs) with a small memory footprint and efficient parallel algorithms for querying and building. (lirmm.fr)
Abstract: New technologies have tremendously increased sequencing throughput compared to traditional techniques, thereby complicating DNA assembly. (lirmm.fr)
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)

Exome sequencing is a laboratory test designed to identify and analyze the sequence of all protein-coding nuclear genes in the genome. (nih.gov)
The diagnostic utility of exome sequencing has consistently been 20%-30% (i.e., a diagnosis is identified in 20%-30% of individuals who were previously undiagnosed but had features suggestive of a genetic condition) [ Gahl et al 2012 , Lazaridis et al 2016 ]. (nih.gov)
A suite of custom software tools have been developed to rapidly integrate, explore, discover and validate molecular profiling data from the NGS modalities of Whole Exome Sequencing (WES) and RNA-seq with each other, as well as with historical microarray and salient clinical datasets. (biomedcentral.com)

This is then a gene-centric assembly where the goal is to assemble reads into contigs for a family of orthologous genes. (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)
A gene-centric assembly for a family of orthologous genes F is the assembly of all reads associated with F . One approach to this is simply to run an existing assembly tool on the reads. (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)
Multigene phylogenies obtained through Sanger sequencing often use barcode sequences, specific genic or intergenic fragments of well-defined genes, that have been widely used over the past decades. (apsnet.org)
In the past ten years, improvements in massively parallel sequencing techniques have led to the development and widespread clinical use of multigene panels, which allow simultaneous testing of two to more than 150 genes. (nih.gov)
These include genes selected by a clinician for analysis by clinical sequencing. (nih.gov)
Results for each gene on the custom multigene panel are reported to the ordering clinician, whereas the results from the remaining genes sequenced (but not requested by the clinician) are not analyzed or included in the final laboratory report. (nih.gov)
We also identified several genes that do not appear to be protein coding, and generated 17 kb of novel transcript sequence data from re-sequencing 97 EST clones. (biomedcentral.com)
The candidate interval was shown to exhibit an extraordinary level of alternate splicing - 19 transcripts were identified for the 5 protein coding genes, but it appears that a significant portion (14/19) of these alternate transcripts did not have an open reading frame, hence their functional role is questionable. (biomedcentral.com)
The fifteen enrofloxacin resistant strains were selected for the PCR to detect the genes gyrA, gyrB, parC, and parE, and genetic sequencing to identify mutations in these genes. (scielo.br)
10 Similarly, in recent studies, at least one third of genes in diverse organisms can exhibit alternative transcription, leading to the production of N-terminally extended proteins or alternative reading frames. (biorxiv.org)
1. Create an "array design" with all genes of interest (ideally this would be the largest set possible, e.g. known genes + predicted genes of all qualities, perhaps even predicted genes from the new sequence data). (lu.se)
Usage of reporter genes need to be specified in iLab before project start and the exact sequence information and gene co-ordinates need to be submitted to be included during sequencing read alignment. (lu.se)

While some of these are made for aligning Illumina Sequence Analyzer reads, none of these are fully utilizing its probability (prb) output. (seqanswers.com)
This usually gives more alignments than running off the fastq files but has been criticised by some as the Illumina fastq files have been quality calibrated but the prb files are not. (seqanswers.com)
Reads from a wide range of sequencing platforms, for example Illumina, Roche-454, Ion Torrent, PacBio or ABI-Sanger, can be processed including paired reads. (debian.net)
After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. (nih.gov)
The amplified viral nucleic acid libraries of the bat species were then sequenced with the Illumina/Solexa GAII sequencer (Illumina, San Diego, CA, USA). (cdc.gov)
Those reads generated by the Illumina/Solexa GAII with length of 80 bases were directly aligned to the protein sequences in the National Center for Biotechnology Information nonredundant protein database by the blastx program in the BLAST software package, version 2.2.22 ( www.ncbi.nlm.nih.gov/blast ) with parameters "-e 1e-5 -F T -b 10 -v 10. (cdc.gov)

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)
Specifically, the user selects a gene family based on a classification such as KEGG and all reads binned to that gene family are assembled. (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)
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)
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)
Often, sequence data of a single barcode gene is not sufficient to specifically determine fungal identity at the species level, whereas a combination of three or more barcodes can reliably determine which species the sample belongs to (see, e.g. (apsnet.org)
according to morphological, physiological and its 16S rRNA gene sequence. (researchgate.net)
Whole transcriptome sequencing (RNA-seq) represents a powerful approach for whole transcriptome gene expression analysis. (biomedcentral.com)
Outside BASE, align the new sequences to genome or transcript sequences and calculate "intensities" for each gene on the "array design" and dump into a tab delimited raw data file. (lu.se)
All 10x Genomic services include a final report containing a Cell Ranger web summary file for quality control (QC) of the sequencing outcome, as well as FASTQ, BAM, gene count matrix containing all single cells or nuclei passing QC, basic visualization and clustering. (lu.se)
But today, programs are starting to use more and more molecular testing and now perform single gene sequencing, employ multi-gene panels, and are beginning to explore the utility of whole exome and genome sequencing. (cdc.gov)

In my final step, I want to assess the per-residue read coverage of the consensus amino acid sequence to demonstrate an idea of confidence in that sequence. (stackexchange.com)
We have been optimising amino acid substitution matrices for protein sequence alignments. (uni-hamburg.de)
Maps are used to visualise physicochemical properties of amino acids in the alignment positions. (lu.se)
Similar kinds of things were done for amino acid sequencing, a very different kind of language. (medscape.com)

20 nucleotides long), sampled at equidistant steps along the genomic reference sequences. (debian.net)

Analyze, modify, and simulate evolutionary sequences. (haskell.org)
force] [--no-elynx-file] COMMAND Analyze, and simulate multi sequence alignments. (haskell.org)
If data is a multi sequence alignment, additionally analyze columns. (haskell.org)
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)

We established the complete genome sequences of 2 betacoronaviruses (Bat Rp-coronavirus/Shaanxi2011 and Bat Cp-coronavirus/Yunnan2011), which are 29,484 nt and 29,452 nt, respectively. (cdc.gov)
Draft Genome Sequences for a Diverse Set of Isolates from 10 Neisseria Species. (cdc.gov)

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)
to find the per base-pair read coverage over a number of isoform contigs from my Trinity assembly . (stackexchange.com)
Hence, assembly programs resort to de Bruijn graphs (dBG) of \(k\)-mers of short reads to compute a set of long contigs, each being a putative segment of the sequenced molecule. (lirmm.fr)

The history and advances of reversible terminators used in new generations of sequencing technology. (nature.com)
Recent advances in DNA sequencing technology have dramatically increased the scale and scope of DNA sequencing. (umd.edu)
Recent advances in nucleic acid sequencing now permit rapid and genome-scale analysis of genetic variation and transcription, enabling population-scale studies of human biology, disease, and diverse organisms. (biorxiv.org)

No genotyping methods were used to confi rm the genetic lated by BFAST), 90% of the reads had to agree. (cdc.gov)
This combination of hybridization with enzymatic removal of 3´ off-target sequence enables greater sequencing specificity relative to conventional hybridization-based enrichment methods. (neb.com)
The methods used in multigene panels may include sequence analysis , deletion/duplication analysis , and/or other non-sequencing-based tests. (nih.gov)
Single-molecule long-read sequencing has the potential to dramatically advance the field, although high error rates are a challenge with existing methods. (deepdyve.com)
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)
My focus has been on the data analysis side of things, employing different computational methods to deal with mapping ambiguity and adapting new technologies such as single-cell RNA sequencing to better understand three families of transposable elements. (lu.se)

Results In the present study, we performed a systematic transcriptome analysis based on the deep RNA sequencing of ten asthmatic children before and after desensitization treatment. (researchsquare.com)
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)

I have also conducted a multiple sequence alignment of those isoforms using Clustal Omega DNA aligner. (stackexchange.com)

Sequence reads were processed and mapped to the mouse genome (mm8) using ELAND pipeline. (nih.gov)

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)
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)
Other types of DNA sequence analysis, as well as preprocessing of the reads for assembly, use classical data structures to index all substrings of the reads. (lirmm.fr)
Phased diploid genome assembly with single-molecule real-time sequencing. (crossref.org)
Assembly of long, error-prone reads using repeat graphs. (crossref.org)
Canu: scalable and accurate long-read assembly via adaptive k-mer weighting and repeat separation. (crossref.org)
No assembly was performed before alignment. (cdc.gov)

Summary: BWA-MEM is a new alignment algorithm for aligning sequence reads or long query sequences against a large reference genome such as human. (arxiv.org)
Finally, a guide sequence library containing reference annotations may also be optionally aligned with the query sequences and used to produce a second maximum-likelihood tree for positive control (smaller guide trees may not always be as accurate as fuller ones, when in doubt add more sequences to the clades of interest). (cdc.gov)

SAMtools implements various utilities for post-processing alignments in the SAM format, such as indexing, variant caller and alignment viewer, and thus provides universal tools for processing read alignments. (nih.gov)
PG2 can be integrated with current and emerging sequencing technologies, assemblers, variant callers, and mass spectral analysis algorithms, and is available open-source from https://github.com/kentsisresearchgroup/ProteomeGenerator2 . (biorxiv.org)
But ensuring sequencing and variant interpretation is done correctly and accurately is vitally important so that newborns, families, and clinicians are given the best available information to direct diagnosis and treatments. (cdc.gov)

Multigene phylogenies constructed from multiplexed and Sanger sequencing data are regularly used in mycology and other disciplines as a cost-effective way of species identification and as a first means to investigate genetic diversity samples. (apsnet.org)
We present AB12PHYLO, an integrated pipeline that can perform all necessary steps from reading raw Sanger sequencing data through visualizing and editing phylogenies. (apsnet.org)
Evolutionary relationships in Cyperaceae have been studied mostly using Sanger sequencing until recently. (frontiersin.org)

Real-time DNA sequencing from single polymerase molecules. (crossref.org)
A second linker was ligated to the MmeI cut sites and ligation-mediated polymerase chain reaction performed prior to being sequenced. (nih.gov)

1998). Biological sequence analysis: probabilistic models of proteins and nucleic acids. (wikipedia.org)

Sequencing and alignment: Sequencing was done by the Functional Genomics Core at the University of Pennsylvania. (nih.gov)

sequencing-uml-draft-1.png ( 74.9 KB ) - added by Nicklas Nordborg 13 years ago . (lu.se)
sequencing-biomaterials-draft-2.png ( 97.7 KB ) - added by Nicklas Nordborg 13 years ago . (lu.se)

The following graphic depicts a typical workflow for preparing, analyzing, and visualizing results from transcriptomic RNA sequencing data. (r-bloggers.com)

For each read, potentially matching segments in the reference are identified from seed matches in the index and subsequently aligned with the read using a banded Smith-Waterman algorithm. (debian.net)
Automatic alignment is based on ClustalV algorithm. (bio.net)
The algorithm is robust to sequencing errors and applicable to a wide range of sequence lengths from 70bp to a few megabases. (arxiv.org)

A mode for the detection of split (chimeric) reads is provided. (debian.net)
It automatically chooses between local and end-to-end alignments, supports paired-end reads and performs chimeric alignment. (arxiv.org)

The project team will work to link together two existing genetic interpretation platforms to produce a solution that will make it easier for NBS programs to add sequencing within their public health laboratories. (cdc.gov)

annotation when starting an alignment so that the bioassay disappears from the "Start masking and alignment" count and list. (lu.se)

Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols. (nih.gov)
Guide sequence libraries are never more than 200 sequences in size. (cdc.gov)

The human exome includes all coding nuclear DNA sequences, approximately 180,000 exons that are transcribed into mature RNA. (nih.gov)

1. Describe the current algorithms and data structures used in bioinformatic sequence analysis. (aber.ac.uk)
2. Perform an analysis of a set of DNA sequences and interpret the results. (aber.ac.uk)
Comparative sequence analysis of pPATH pathogenicity plasmids in Pantoea agglomerans gall-forming bacteria. (tau.ac.il)
Before subsequent analysis, edundant reads in each genomic position were condenced into one to avoid possible PCR bias or each sample. (nih.gov)
ProMSED is an easy-to-use application for Windows 3.x/95 that performs automatic and manual multiple protein sequences alignment, alignment analysis and editing. (bio.net)
ProMSED can align complete set of sequences, its subset and any selected block, providing thus flexible tool for sequences analysis, visualization, edition and illustrations preparation. (bio.net)
However, most proteomic studies rely on consensus databases to match spectra to peptide and proteins sequences, and thus remain limited to the analysis of canonical protein sequences. (biorxiv.org)

Do/can the paired-end reads have overlaps? (stackexchange.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)

What can be the bias of aligning paired-reads in a single-end mode? (stackexchange.com)

Each group of sub-experiments tested fifteen combinations of three different word sizes (7, 11, and 15) and five different e-values (1000, 10, 0.1, 0.001, and 0.00001) for a total of 1.2 million attempted genome-wide alignments. (icr.org)

Microbiome sequencing projects typically collect tens of millions of short reads per sample. (biomedcentral.com)
However, RNA-seq carries a few limitations, e.g., the requirement of a significant amount of input RNA and complications led by non-specific mapping of short reads. (biomedcentral.com)

This list of sequence alignment software is a compilation of software tools and web portals used in pairwise sequence alignment and multiple sequence alignment. (wikipedia.org)
Today, a number of tools exist for each of the steps for multigene phylogenetic analyses, including quality control and trimming, the generation of a multiple sequence alignment (MSA), extraction of informative sites, and the construction of the final phylogenetic tree. (apsnet.org)
Multiple sequence alignment as a sequence-to-sequence learning problem. (tau.ac.il)
Subject: ANNOUNCEMENT: Protein Multiple Sequences Editor for Win 3.x/95 Dear All, With the increasing of protein sequence data, multiple alignment is one of the important techniques to understand protein structure-function organization and evolution. (bio.net)
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)
http://pbil.univ-lyon1.fr/software/seaview.html Summary : Graphical multiple sequence alignment editor Description : SeaView is a graphical multiple sequence alignment editor developed by Manolo Gouy. (redhat.com)
Multiple sequence alignment averaging improves phylogeny reconstruction. (cdc.gov)
MultiDisp is a tool for analysing and visualising multiple sequence alignments (MSAs). (lu.se)
Also use DISTINCT when counting or loading the list since otherwise the same bioassay will appear multiple times after a re-alignment. (lu.se)

Visualises polarity of residues in MSA alignment positions. (lu.se)

See structural alignment software for structural alignment of proteins. (wikipedia.org)
Our web server is running and does threading using a mixture of sequence terms and a structural term based on Bayesian classification of fragment properties. (uni-hamburg.de)

Such genotyping tools are useful for molecular ep- nome sequence typing (WGST) as a viable and discrimina- idemiologic studies, microbial forensics, and phylogenetic tory tool for genotyping and molecular epidemiologic analy- applications. (cdc.gov)
Evolutionary sequences and phylogenetic trees can be read, viewed, modified and simulated. (haskell.org)
Simulate multi sequence alignments along phylogenetic trees. (haskell.org)

Additionally, a BLAST search in a reference database is often performed to identify sequences of type specimens to compare the samples within the phylogeny. (apsnet.org)
SMALT efficiently aligns DNA sequencing reads with a reference genome. (debian.net)
Read alignment maps short DNA sequences to a reference genome to discover conserved and polymorphic regions of the genome. (umd.edu)
reference sequence ( for inst. (bio.net)

The emphasis will be on the computational algorithms that allow us to discover information from biological sequence. (aber.ac.uk)

How to estimate whether a long-read is meaningful sequence? (stackexchange.com)
Short read and long read sequencing. (aber.ac.uk)
The evolutionary dynamics that retain long neutral genomic sequences in face of indel deletion bias: a model and its application to human introns. (tau.ac.il)
NGMLR and Sniffles can automatically filter false events and operate on low-coverage data, thereby reducing the high costs that have hindered the application of long reads in clinical and research settings. (deepdyve.com)
I have used various RNA and DNA-based technologies, including both short-read and long-read sequencing techniques, and worked to integrate these datasets, including bulk and single-cell datasets. (lu.se)

Our results demonstrate that data generated with a family-specific kit do not necessarily have more power than those obtained with a universal kit, but that data generated with different targeted sequencing kits can often be merged for downstream analyses. (frontiersin.org)
These metagenomic shotgun reads of mammalian origin were excluded from our analyses of agricultur al dust microbiota. (cdc.gov)

GenBank release 225: Over 1 billion sequence records stored! (cdc.gov)

DNA sequence alignment showed that 19% or 62% of shotgun pyrosequencing metagenomic DNA sequence reads from swine facility or household dusts, respectively, were of swine or human origin, respectively. (cdc.gov)

Targeted sequencing has emerged as a strong tool for estimating species trees in the face of rapid radiations, lineage sorting, and introgression. (frontiersin.org)

RNASeq read coverage in protein space? (stackexchange.com)

Anatomy4

Organisms13

Diseases2

Chemicals and Drugs32

Analytical, Diagnostic and Therapeutic Techniques and Equipment41

Psychiatry and Psychology1

Phenomena and Processes76

Disciplines and Occupations4

Anthropology, Education, Sociology and Social Phenomena1

Technology, Industry, Agriculture4

Information Science41

Health Care16

High-throughput4

Genomes8

Whole Genome Sequencing3

Next-Generation Sequencing7

Bioinformatics3

Protein alignments1

FASTA4

Variants3

Nucleotide9

Similarity6

Abstract4

Exome Sequencing3

Genes15

Illumina6

Gene13

Amino4

Genomic reference1

Analyze4

Genome sequences2

Contigs3

Advances3

Methods6

Transcriptome analysis2

CLUSTAL1

Mapped to the mouse genome1

Assembly8

Query sequences2

Variant3

Sanger3

Polymerase2

Nucleic1

Genomics1

Nicklas Nordborg2

Workflow1

Algorithm3

Chimeric2

Genetic1

Annotation1

Libraries2

Exons1

Analysis7

Overlaps1

Platforms1

Aligning paired-reads1

10001

Short reads2

Multiple9

Residues1

Structural2

Phylogenetic3

Reference4

Algorithms1

Long5

Analyses2

GenBank1

Metagenomic1

Species1

RNASeq1