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*  Transcriptome analysis of the honey bee fungal pathogen, Ascosphaera apis: implications for host pathogenesis.
Molecular Sequence Annotation. Multigene Family / genetics. Onygenales / genetics*, pathogenicity. Phylogeny. Protein Structure ... The Maker annotation pipeline [9] was used to annotate the A. apis genome [7]. Maker masked repetitive sequences with ... Following the sequencing of the A. apis genome in 2006 [7], our comprehensive, transcriptome-informed gene annotations ... Manual annotation methods Transcripts were compared to sequences in GenBank. TBLASTX and BLASTX searches were done against ...
http://www.biomedsearch.com/nih/Transcriptome-analysis-honey-bee-fungal/22747707.html
*  Conceptual and ortholog-based maximum likelihood phylog | Open-i
Molecular Sequence Annotation. *Phenotype. *Phylogeny. *Proteome/genetics. *Sequence Analysis, DNA. *Trichothecenes/genetics ... Ideally these annotations would be supported by RNA data, but the RNA extractable from each of the four strains was too ... Ideally these annotations would be supported by RNA data, but the RNA extractable from each of the four strains was too ... Mentions: The phylogeny of the four Stachybotrys strains that were sequenced is shown in Figure 2A. The strains include two ...
https://openi.nlm.nih.gov/detailedresult.php?img=PMC4117958_12864_2013_6290_Fig2_HTML&req=4
*  Population split and historical mixture for Tibetan pig | Open-i
Molecular Sequence Annotation. *Polymorphism, Single Nucleotide. *Principal Component Analysis. *Receptors, N-Methyl-D- ...
https://openi.nlm.nih.gov/detailedresult.php?img=PMC4197311_12864_2014_6536_Fig2_HTML&req=4
*  ZFIN Publication: Howe et al., 2013
Molecular Sequence Annotation. *Pseudogenes/genetics. *Reference Standards. *Sex Determination Processes/genetics. *Zebrafish/ ... To examine this, we generated a high-quality sequence assembly of the zebrafish genome, made up of an overlapping set of ... Detailed automatic and manual annotation provides evidence of more than 26,000 protein-coding genes, the largest gene set of ... The zebrafish reference genome sequence and its relationship to the human genome ...
http://zfin.org/ZDB-PUB-130425-8
*  VU Faculties - Research Output - Vrije Universiteit Amsterdam
Molecular Sequence Annotation Humanities need a replication drive too. Peels, R. & Bouter, L., 21 Jun 2018, In : Nature. 558, ... Single-cell isoform RNA sequencing characterizes isoforms in thousands of cerebellar cells. Gupta, I., Collier, P. G., Haase, B ...
https://research.vu.nl/en/organisations/vu-faculties-2/publications/?type=%2Fdk%2Fatira%2Fpure%2Fresearchoutput%2Fresearchoutputtypes%2Fcontributiontojournal%2Fletter
*  OPUS at UTS: Complete Genome Sequence of the Cystic Fibrosis Pathogen Achromobacter xylosoxidans NH44784-1996 Complies with...
Molecular Sequence Annotation. en_US. dc.subject.mesh. Achromobacter denitrificans. en_US. ... Complete Genome Sequence of the Cystic Fibrosis Pathogen Achromobacter xylosoxidans NH44784-1996 Complies with Important ... Complete Genome Sequence of the Cystic Fibrosis Pathogen Achromobacter xylosoxidans NH44784-1996 Complies with Important ... Complete genome sequence of the cystic fibrosis pathogen Achromobacter xylosoxidans NH44784-1996 complies with important ...
https://opus.lib.uts.edu.au/handle/10453/117604
*  OPUS at UTS: Circleator: Flexible circular visualization of genome-associated data with BioPerl and SVG - Open Publications of...
Molecular Sequence Annotation. en_US. dc.subject.mesh. Polymorphism, Single Nucleotide. en_US. ... i) visualizing gene annotation and DNA sequence data from a GenBank flat file, (ii) displaying patterns of gene conservation in ... i) visualizing gene annotation and DNA sequence data from a GenBank flat file, (ii) displaying patterns of gene conservation in ... It leverages BioPerl to support standard annotation and sequence file formats and produces publication-quality SVG output. It ...
https://opus.lib.uts.edu.au/handle/10453/33898
*  Home - Publications
Gene expression regulation; Molecular sequence annotation; Parkinson disease. *Gene expression; Lipoproteins; Liver; Metabolism ... Base sequence; Conserved sequence; Genome; Regulatory sequences; RNA Splicing; Terminator regions (Genetics) ... Annotation. *Anti-allergic agents; Automatic data processing; Gene expression profiling; Gene expression regulation; ... Algorithms; Oligonucleotide array sequence analysis; Regression analysis; Reproducibility of results; Statistics. *Altitude; ...
https://livingsystems.kaust.edu.sa/Pages/Publications.aspx?y=2007
*  Carol R Buell - Publications - MSU Scholars
Plant genome annotation methods. Ouyang, S., Thibaud-Nissen, F., Childs, K. L., Zhu, W. & Buell, C. R. 2009 Methods in ... Chan, A. P., Rabinowicz, P. D., Quackenbush, J., Buell, C. R. & Town, C. D. Nov 1 2007 Methods in Molecular Biology. Vol. 406, ... Molecular Biology. Vol. 513, p. 263-282 20 p. (Methods in Molecular Biology; vol. 513). Research output: Research › Chapter ... Structural, Functional, and Comparative Annotation of Plant Genomes. Thibaud-Nissen, F., Wortman, J., Buell, C. R. & Zhu, W. ...
https://scholars.opb.msu.edu/en/persons/carol-r-buell-2/publications/?type=%2Fdk%2Fatira%2Fpure%2Fresearchoutput%2Fresearchoutputtypes%2Fcontributiontobookanthology%2Fchapter
*  McCarthy, F. M.<...
Molecular Sequence Annotation Medicine & Life Sciences Chickens Medicine & Life Sciences Proteins Medicine & Life Sciences ... RNA sequencing exposes adaptive and immune responses to intrauterine growth restriction in fetal sheep islets. Kelly, A. C., ...
https://arizona.pure.elsevier.com/en/persons/fiona-m-mccarthy
*  Curation of the genome annotation of Pichia pastoris (Komagataella phaffii) CBS7435 from gene level to protein function<...
Detailed analysis of sequence alignment and protein domain predictions were made to extend the functional genome annotation to ... Detailed analysis of sequence alignment and protein domain predictions were made to extend the functional genome annotation to ... Detailed analysis of sequence alignment and protein domain predictions were made to extend the functional genome annotation to ... Detailed analysis of sequence alignment and protein domain predictions were made to extend the functional genome annotation to ...
https://graz.pure.elsevier.com/en/publications/curation-of-the-genome-annotation-of-pichia-pastoris-komagataella
*  Identification of Simple Sequence Repeat Biomarkers through Cross-Species Comparison in a Tag Cloud Representation
... gene annotations, and molecular functions. To lay emphasis on identification of consensus and unique features of SSRs among ... S. Hennig, D. Groth, and H. Lehrach, "Automated gene ontology annotation for anonymous sequence data," Nucleic Acids Research, ... Genome Sequences. To obtain genome sequences of various organisms, the developed system employed Ensembl release 65 as the ... gene annotation, sequence contents, and corresponding translated proteins through a fast, responsive, and user-friendly web ...
https://www.hindawi.com/journals/bmri/2014/678971/
*  The UK10K project identifies rare variants in health and disease. - Nuffield Department of Population Health
We describe population structure and functional annotation of rare and low-frequency variants, use the data to estimate the ... In extensively phenotyped cohorts we characterize over 24 million novel sequence variants, generate a highly accurate ... benefits of sequencing for association studies, and summarize lessons from disease-specific collections. Finally, we make ... Here we describe insights from sequencing whole genomes (low read depth, 7×) or exomes (high read depth, 80×) of nearly 10,000 ...
https://www.ndph.ox.ac.uk/publications/570702
*  Revised sequence and annotation of the Rhodobacter sphaeroides 2.4.1 genome. - PubMed - NCBI
Molecular Biology Databases. *REBASE ref# 15306 - REBASE - The Restriction Enzyme Database. Research Materials. *online strain ... Revised sequence and annotation of the Rhodobacter sphaeroides 2.4.1 genome.. Kontur WS1, Schackwitz WS, Ivanova N, Martin J, ... The DNA sequences of chromosomes I and II of Rhodobacter sphaeroides strain 2.4.1 have been revised, and the annotation of the ... Errors in the originally published sequence have been corrected, and ~11% of the coding regions in the original sequence have ...
https://www.ncbi.nlm.nih.gov/pubmed/23209255
*  02133409 | Yearbooks 2018 | University of Pretoria
Genome project design, DNA sequencing methods and annotation. Molecular evolution. Phylogenetic inference methods. Applications ... Protein purification and characterization including, pI, molecular mass, amino acid composition and sequence. Practical ... Auto-immunity: Molecular mechanisms of the maintenance and failure of the recognition of foreign in the context of self in the ... Molecular structure and chemical bonding using the VSEOR model. Nomenclature of inorganic ions and compounds. Classification of ...
https://www.up.ac.za/yearbooks/2018/programmes/view/02133409
*  GTS 354 | Yearbooks 2019 | University of Pretoria
Genome project design, DNA sequencing methods and annotation. Molecular evolution. Phylogenetic inference. Applications of ... Comparison of the molecular organisation of viral, archaea, bacterial and eukaryotic genomes. ...
https://www.up.ac.za/yearbooks/2019/modules/view/GTS%20354
*  Evolutionary history of Tibetans inferred from whole-genome sequencing. - Physiology, Anatomy and Genetics
We sequenced the whole-genomes of 27 Tibetans and conducted analyses to infer a detailed history of demography and natural ... Molecular Sequence Annotation, Proteins, Receptors, Calcitriol, Selection, Genetic, Tibet ... Evolutionary history of Tibetans inferred from whole-genome sequencing. Hu H., Petousi N., Glusman G., Yu Y., Bohlender R., ... We sequenced the whole-genomes of 27 Tibetans and conducted analyses to infer a detailed history of demography and natural ...
https://www.dpag.ox.ac.uk/publications/692374
*  Sequencing papaya X and Yh chromosomes reveals molecular basis of incipient sex chromosome evolution | PNAS
Gene Annotation.. The repeat-masked HSY and X sequences were blasted to the papaya EST and gene model databases, and EST ... Individual BAC clones were sequenced using Sanger sequencing method. Escherichia coli genomic sequences, vector sequences, low ... close to the sequencing error of 1 per 105 nucleotides (SI Appendix, Fig. S2B). The molecular HSY border B, where sequence ... Sequencing papaya X and Yh chromosomes reveals molecular basis of incipient sex chromosome evolution. Jianping Wang, Jong-Kuk ...
https://www.pnas.org/content/109/34/13710
*  Molecular Vision: Expression profiles during dedifferentiation in newt lens regeneration revealed by expressed sequence tags
... and functions are also assigned to sequences with GO annotations as part of the annotation process. The annotations were ... Functional annotation. Functional annotation of the assembled sequences was performed using the Blast2GO program with default ... Sequencing, assembly, and functional annotation of newt expression sequence tags. As mentioned previously dedifferentiation ... The initial set of cDNA sequence reads were 10,449 (Table 1). The total length of these sequences was 9.85 Mb, which was ...
http://www.molvis.org/molvis/v16/a9/
*  EMBOSS: edamhasinput
Sequence annotation namespace: operation def: Annotate a molecular sequence record with terms from a controlled vocabulary. ... one or more molecular sequences and associated annotation. subset: operations synonym: "Sequence processing (general)" EXACT [ ... "Applies to both pure/raw sequences and sequence records. Indirectly also to sequence sets or IDs (?)"} ! Sequence relationship ... Term] id: EDAM_operation:2403 name: Sequence analysis namespace: operation def: Analyse one or more known molecular sequences. ...
http://emboss.sourceforge.net/apps/release/6.5/emboss/apps/edamhasinput.html
*  About | jalview.org
It can also work with sequence annotation, secondary structure information, phylogenetic trees and 3D molecular structures. ... and Jalview's own sequence and alignment annotation format. It allows editing, and can also show the consensus sequence, ... JalviewLite allows sequence alignments to be visualized in a web page, along with annotation, phylogenetic trees, and ... The Desktop can access sequence, alignment, 3D structure and annotation databases, and web services for multiple alignment, ...
http://www.jalview.org/about
*  LNCipedia: a database for annotated human lncRNA transcript sequences and structures. - PubMed - NCBI
Molecular Sequence Annotation. *Proteins/genetics. *RNA, Long Noncoding/chemistry*. *RNA, Long Noncoding/genetics ... Different high-throughput methods to identify new lncRNAs (including RNA sequencing and annotation of chromatin-state maps) ... LNCipedia: a database for annotated human lncRNA transcript sequences and structures.. Volders PJ1, Helsens K, Wang X, Menten B ... LNCipedia is publicly available and allows users to query and download lncRNA sequences and structures based on different ...
https://www.ncbi.nlm.nih.gov/pubmed/23042674?access_num=23042674&link_type=MED&dopt=Abstract
*  MAKER2: an annotation pipeline and genome-database management tool for second-generation genome projects. - PubMed - NCBI
Molecular Sequence Annotation. *Plants/genetics. *Software*. Grant support. *R01-HG004694/HG/NHGRI NIH HHS/United States ... Re-annotation of a portion of the Maize genome using MAKER2. Annotation Edit Distance (AED) provides a measurement for how well ... Evaluating AED as a metric for annotation quality control. Annotation Edit Distance (AED) provides a measurement for how well ... We also show that MAKER2 can evaluate the quality of genome annotations, and identify and prioritize problematic annotations ...
https://www.ncbi.nlm.nih.gov/pubmed/22192575?dopt=Abstract
*  RCSB PDB: Molecular Graphics Software Links
Users can perform simple and advanced searches based on annotations relating to sequence, structure and function. These ... Protein structure annotation using sequence profiles * POLYVIEW-3D. Versatile annotation and high quality visualization of ... Align proteins by sequence and 3D structure. * Swiss PDB viewer A 3D graphics and molecular modeling program for the ... Zeus provides a sequence search that can highlight within the molecular structure. Ramachandran plots of internal dihedral ...
https://www.rcsb.org/pages/thirdparty/molecular_graphics
*  SMART, a simple modular architecture research tool: Identification of signaling domains | PNAS
Annotation of molecular function in sequence databases and even in the literature is difficult to interpret given that the term ... automatic sequence annotation. The functions of only a small fraction of known proteins have been determined by experiment. As ... Of all protein sequence databases, SwissProt is the most extensively annotated, making use of literature- and sequence-derived ... As the set of signaling sequences is necessarily incomplete and as there may be other domains represented in the query sequence ...
https://www.pnas.org/content/95/11/5857?ijkey=97b0db2c11a77653d3aaabb9ad7527f6193be03b&keytype2=tf_ipsecsha