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*  Rapid Whole-Genome Sequencing for Surveillance of Salmonella enterica Serovar Enteritidis - Volume 20, Number 8-August 2014 -...
Although whole-genome sequencing has been found to improve discrimination of outbreak clusters, whether this procedure can be ... Whole-genome sequencing identified additional isolates that could be attributed to the outbreak, but which differed from the ... Additional cases could be attributed to the outbreak strain on the basis of whole-genome data. The prospective study included ... Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics. 2009;25:1754-60. DOIPubMed ...
  https://wwwnc.cdc.gov/eid/article/20/8/13-1399_article
*  pairwise sequence alignment tool :: Multiple Sequence Alignment - CLUSTALW :: Pairwise Alignment: FAST/APPROXIMATE SLOW...
Multiple Sequence Alignment - CLUSTALW Description:. Pairwise Alignment: FAST/APPROXIMATE SLOW/ACCURATE. Enter your sequences ( ... "align.genome.jp"'s top keywords pairwise sequence alignment tool blast searches blast protein sequence blast dna sequence ... www1.emsjane.com: emt training centers continuing education coordinating board for emergency medical services ... protein alignments blast basic local alignment search tool clustalw alignment score multiple sequence alignment algorithm ad.jp ...
  http://www.topseostats.com/site/align.genome.jp
*  Preprocessing and Quality Control for Whole-Genome Sequences from the Illumina HiSeq X Platform | SpringerLink
The advancement of high-throughput sequencing technologies enables sequencing of human genomes at steadily decreasing costs and ... Li H et al (2009) The sequence alignment/map format and samtools. Bioinformatics 25:2078-2079. doi: 10.1093/bioinformatics/ ... Bentley DR et al (2008) Accurate whole human genome sequencing using reversible terminator chemistry. Nature 456:53-59. doi: ... The work presented in this chapter was supported by the German Centre for Cardiovascular Research (DZHK; Deutsches Zentrum für ...
  https://link.springer.com/protocol/10.1007/978-1-4939-7274-6_30
*  Multiple sequence alignment - Wikipedia
However, as the number of sequences increases and especially in genome-wide studies that involve many MSAs it is impossible to ... a fast and accurate multiple sequence alignment algorithm. Multiple sequence alignment lectures - from the Max Planck Institute ... "Genetic analysis software". National Center for Biotechnology Information. Retrieved March 3, 2010. Hogeweg P, Hesper B (1984 ... tree alignment Phylogenetics Sequence alignment software Multiple sequence alignment viewers Structural alignment Alignment- ...
  https://en.wikipedia.org/wiki/Multiple_sequence_alignment
*  Comparison of solution-based exome capture methods for next generation sequencing | Genome Biology | Full Text
A control DNA sample was captured with all four capture methods and prepared for Illumina GAII sequencing. Sequence data from ... We developed a bioinformatics pipeline for quality control, short read alignment, variant identification and annotation of the ... High GC content of the target sequence was associated with poor capture success in all exome enrichment methods. Comparison of ... accuracy when compared to common SNPs on genome-wide association arrays. Libraries captured with NimbleGen kits aligned more ...
  https://genomebiology.biomedcentral.com/articles/10.1186/gb-2011-12-9-r94
*  Cxcl8 (IL-8) Mediates Neutrophil Recruitment and Behavior in the Zebrafish Inflammatory Response | The Journal of Immunology
Further genomic DNA analysis was performed to obtain accurate exon/intron sequences. Protein sequence alignments of zebrafish ... Next, after confirming the full coding sequence, we performed a BLAST search of the zebrafish genome from Ensembl using the zv9 ... Medical Research Council Centre for Developmental and Biomedical Genetics, University of Sheffield, Sheffield S10 2TN, United ... This sequence is shown in Supplemental Video 1. Scale bar, 100 μm. (B) Counts of fluorescent neutrophils at the wound were made ...
  http://www.jimmunol.org/content/190/8/4349.full
*  Characterization of Brucella abortus mutant strain Δ22915, a potential vaccine candidate | Veterinary Research | Full Text
Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol 10:R25View ArticlePubMedPubMed ... Li B, Dewey CN (2011) RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome. BMC ... flanking the gene coding sequence, and primer pair BAB_RS22915 OF/BAB_RS22915 OR, partially overlapping the deleted sequence, ... Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou, China ...
  https://veterinaryresearch.biomedcentral.com/articles/10.1186/s13567-017-0422-9
*  A high-throughput sequencing test for diagnosing inherited bleeding, thrombotic, and platelet disorders | Blood Journal
Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 2009;25(14):1754-1760. ... whole genome sequencing (WGS)2 and targeted sequencing of pre-specified regions of the genome by means of probe-based capture. ... Clinical Research Center, National Hospital Organization Nagoya Medical Center, Nagoya, Japan; *Find this author on Google ... Detection and sequence of mutations in the factor VIII gene of haemophiliacs. Nature 1985;315(6018):427-430. ...
  http://www.bloodjournal.org/content/127/23/2791?sso-checked=true
*  AdapterRemoval: easy cleaning of next-generation sequencing reads | BMC Research Notes | Full Text
Furthermore, it can look for adapter sequence in both the 5' and 3' ends of the reads. This is a flexible tool that can be ... the partial or complete sequencing of adapter sequences. These adapter sequences have to be removed as they can hinder correct ... AdapterRemoval is a comprehensive tool for analyzing next-generation sequencing data. It exhibits good performance both in ... With the advent of next-generation sequencing there is an increased demand for tools to pre-process and handle the vast amounts ...
  https://bmcresnotes.biomedcentral.com/articles/10.1186/1756-0500-5-337
*  Pharmacomicrobiomics - Wikipedia
Reads may overlap and prevent accurate alignment to reference genomes. In addition, reads may be contaminated by human DNA ... The sequence of 16S rRNA consists of highly conserved sequences which alternate with nine windows of "hypervariable regions". ... Establish a Data Analysis and Coordinating Center to provide publicly available information about the project, outcomes, and ... and then performing whole genome sequencing (WGS). Reads can be assembled de novo or using reference genomes. However, SMS is ...
  https://en.wikipedia.org/wiki/Pharmacomicrobiomics
*  TopHat (bioinformatics) - Wikipedia
TopHat is a bioinformatic sequence analysis package tool for fast and high throughput alignment of shotgun cDNA sequencing ... accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions". Genome Biology. 14 (4): R36. ... Center for Computational Biology at Johns Hopkins University who together in 2013 also came up with TopHat2 which does accurate ... alignment of transcriptomes in the presence of insertions, deletions and gene fusions. Bowtie (sequence analysis) Trapnell, C ...
  https://en.wikipedia.org/wiki/TopHat_(bioinformatics)
*  Targeted Locus Amplification and Next-Generation Sequencing | SpringerLink
Despite developments in targeted and whole-genome sequencing, the robust detection of all genetic variation, including ... 1.Leiden Genome Technology Center, Department of Human GeneticsLeiden University Medical CenterLeidenThe Netherlands ... Li H, Handsaker B, Wysoker A et al (2009) The sequence alignment/map format and SAMtools. Bioinformatics 25:2078-2079CrossRef ... Li H, Durbin R (2009) Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 25:1754-1760 ...
  https://link.springer.com/protocol/10.1007/978-1-4939-6442-0_13
*  Algorithms accessible via Chinook - Canada's Michael Smith Genome Sciences Centre
T-Coffee: A novel method for fast and accurate multiple sequence alignment. J Mol Biol 302: 205-217. Primer Prediction. Primer3 ... Identifying DNA and protein patterns with statistically significant alignments of multiple sequences. Bioinformatics 15: 563- ... CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific ... LAGAN and Multi-LAGAN: efficient tools for large-scale multiple alignment of genomic DNA. Genome Res 13: 721-731. Mauve Darling ...
  http://www.bcgsc.ca/project/bomge/chinook/algorithms
*  Enabling next-generation sequencing applications with IBM Storwize V7… - English
Learn about enabling next-generation sequencing applications with IBM Storwize V7000 Unified and SONAS Gateway solutions. This ... Both algorithms do gapped alignment. They are usually more accurate and faster on queries with low error rates. Trinity Trinity ... Human genome The human genome includes a complete set of human genetic information stored as separate DNA sequences in 23 ... known as a sequence), which clearly summarizes much of the atomic-level structure of the sequenced molecule. DNA sequencing is ...
  https://www.slideshare.net/IBMIndiaSS/enabling-next-generationapplicationsstorwizeunifiedsonasgatewaysolutions
*  Exome sequencing study in patients with multiple sclerosis reveals variants associated with disease course | Springer for...
The sequence ontology: a tool for the unification of genome annotations. Genome Biol. 2005;6:R44.CrossRefPubMedPubMedCentral ... Li H, Durbin R. Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics. 2009;25:1754-60.CrossRef ... The first validation cohort included 194 MS patients from 7 MS centers [Bilbao (n = 56); UCSF (n = 55); Madrid-Hospital Clínico ... The genome analysis toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. Genome Res. 2010;20:1297- ...
  https://rd.springer.com/article/10.1186%2Fs12974-018-1307-1
*  Similar articles for PubMed (Select 19907642) - PubMed - NCBI
SAP--a sequence mapping and analyzing program for long sequence reads alignment and accurate variants discovery. ... Efficient alignment of pyrosequencing reads for re-sequencing applications.. Fernandes F, da Fonseca PG, Russo LM, Oliveira AL ... National Center for Biotechnology Information, U.S. National Library of Medicine 8600 Rockville Pike, Bethesda MD, 20894 USA ... Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G, Durbin R; 1000 Genome Project Data Processing ...
  https://www.ncbi.nlm.nih.gov/pubmed?linkname=pubmed_pubmed&from_uid=19907642
*  Algorithms currently supported by the Sockeye Platform (through Chinook) - Canada's Michael Smith Genome Sciences Centre
T-Coffee: A novel method for fast and accurate multiple sequence alignment. J Mol Biol 302: 205-217. Annotations. Eponine ... Multi-species Conserved Sequences. MCS Analysis E.H. Margulies, M. Blanchette, NISC Comparative Sequencing Program, D. Haussler ... CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific ... LAGAN and Multi-LAGAN: efficient tools for large-scale multiple alignment of genomic DNA. Genome Res 13: 721-731. Mauve Darling ...
  http://www.bcgsc.ca/project/bomge/sockeye/algorithms
*  Oculus: faster sequence alignment by streaming read compression | BMC Bioinformatics | Full Text
... alignment, and decompression of input sequences. This nearly lossless process (> 99.9%) led to alignment speedups of up to 270 ... Computation may become the bottleneck of genome analysis if growing alignment costs are not mitigated by further improvement in ... Much gain has been gleaned from indexing and compressing alignment databases, but many widely used alignment tools process ... the exponential growth of nucleotide sequencing throughput threatens to outpace bioinformatic analysis. ...
  https://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-13-297
*  Phylogenetic characterisation of circulating, clinical influenza isolates from Bali, Indonesia: preliminary report from the...
There were some strong phylogenetic links with sequences from samples collected in geographically proximal regions, with some ... strains circulating in geographically neighbouring areas as would be expected to occur within a busy regional transit centre. ... In addition to standard clinical and molecular methods for influenza typing, next generation sequencing and subsequent de novo ... genome assembly were performed to investigate the phylogeny of the collected patient samples. The samples collected are ...
  https://bmcinfectdis.biomedcentral.com/articles/10.1186/s12879-017-2684-2
*  Genome project - Wikipedia
... a complete genome sequence will involve 46 separate chromosome sequences. The Human Genome Project was a landmark genome ... 150+ genome resequencing project 100K Genome Project Genomics England Joint Genome Institute Model organism National Center for ... there are still likely to be errors present because DNA sequencing is not a completely accurate process. It could also be ... alignment, SNP detection, resequencing, indel finding, and structural variation analysis. Since the 1980s, molecular biology ...
  https://en.wikipedia.org/wiki/Genome_project
*  PROMALS web server for accurate multiple protein sequence alignments. - PubMed - NCBI
Reference Sequences. *Gene Expression Omnibus. *Genome Data Viewer. *Human Genome. *Mouse Genome ... National Center for Biotechnology Information, U.S. National Library of Medicine 8600 Rockville Pike, Bethesda MD, 20894 USA ... PROMALS web server for accurate multiple protein sequence alignments.. Pei J1, Kim BH, Tang M, Grishin NV. ... PROMALS web server for accurate multiple protein sequence alignments. Nucleic Acids Res. 2007 Jul;35(Web Server issue):W649- ...
  https://www.ncbi.nlm.nih.gov/pubmed/17452345
*  JoVE | Peer Reviewed Scientific Video Journal - Methods and Protocols
Genome sequencing projects have ciphered millions of protein sequence, which require knowledge of their structure and function ... MSAProbs is currently the most accurate alignment algorithm, but its effectiveness is obtained at the expense of computational ... relative to the native sequence. Protein design lies at the center of current advances drug design and discovery. Not only does ... Multiple sequence alignment is a crucial task in a number of biological analyses like secondary structure prediction, domain ...
  https://www.jove.com/visualize/abstract/24586435/quickprobs-fast-multiple-sequence-alignment-algorithm-designed-for
*  A method for positive forensic identification of samples from extremely low-coverage sequence data | BMC Genomics | Full Text
Accurate typing of short tandem repeats from genome-wide sequencing data and its applications. Genome Res. 2015;25:736-49. ... sequenced as part of Platinum Genomes by Illumina, Inc [27] from the National Center for Biotechnology Information Sequence ... The Sequence Alignment/Map format and SAMtools. Bioinformatics. 2009;25:2078-9.PubMed CentralView ArticlePubMedGoogle Scholar. ... Gansauge M, Meyer M. Selective enrichment of damaged DNA molecules for ancient genome sequencing. Genome Res. 2014;24:1543-1549 ...
  https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-015-2241-6
*  UNDR ROVER - a fast and accurate variant caller for targeted DNA sequencing | BMC Bioinformatics | Full Text
... a FASTA format file containing the reference genome sequence, and paired FASTQ files containing sequence reads. Primer ... ROVER is applied to MPS data in BAM format and, therefore, relies on sequence reads being mapped to a reference genome. In this ... The primer-intervening sequence of each read is compared against the reference sequence from the same location and variants are ... In one indicative sequencing experiment, UNDR ROVER (in its fastest mode) required 8-fold less sequential computation time than ...
  https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-016-1014-9
*  Genome sequence of a diabetes-prone rodent reveals a mutation hotspot around the ParaHox gene cluster | PNAS
... with the aligned sequence being filtered and passed to GeneWise (34) to identify accurate spliced alignments. GLEAN (35) was ... and the Oxford Genomics Centre for GC-rich sequencing. This work was funded principally by the European Research Council under ... Sand rat GC values based on transcriptome and genome sequences; when partial only alignable sequence is compared. (D) Unrooted ... Genome sequence of a diabetes-prone rodent reveals a mutation hotspot around the ParaHox gene cluster. Adam D. Hargreaves, Long ...
  http://www.pnas.org/content/114/29/7677