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Toward richer metadata for microbial sequences: replacing strain-level NCBI taxonomy taxids with BioProject, BioSample and...
In later steps of the genome submission process, users provide sequence data and functional annotation that connect to the ... using a taxid as a key to retrieve the genome and associated project metadata was a reasonable approach. However, with next- ... the European Molecular Biology Laboratory, and the Ministry of Education, Culture, Sports, Science and Technology of Japan ( ... ArrayExpress update-trends in database growth and links to data analysis tools. Nucleic Acids Res. 2013; 41:D987-D990 View ...http://standardsingenomics.org/content/9/3/1275/
List of sequenced bacterial genomes - Wikipedia
For the genomes of archaea see list of sequenced archaeal genomes. Genome project Human microbiome project List of sequenced ... 2003). "The genome sequence of Blochmannia floridanus: comparative analysis of reduced genomes". Proc. Natl. Acad. Sci. U.S.A. ... 2006). "Molecular genetic anatomy of inter- and intraserotype variation in the human bacterial pathogen group A Streptococcus ... 2006). "Escherichia coli K-12: a cooperatively developed annotation snapshot-2005". Nucleic Acids Res. 34 (1): 1-9. doi:10.1093 ...https://en.wikipedia.org/wiki/List_of_sequenced_bacterial_genomes
Research at the RBVI
Applications range from small, targeted sequencing projects to genome annotation to large-scale metagenomics analyses. ... TR&D 2: Software for Interactive Analysis of Large Molecular Assemblies. This project continues our successful development of ... Previously, large sequencing projects were the exclusive domain of a few dozen genome centers in the US and around the world. ... The DeRisi lab has several ongoing whole genome and metagenomic sequencing and assembly projects that can provide real-world, ...http://www.cgl.ucsf.edu/Research/index.html
The Cancer Genome Atlas API How To's | ProgrammableWeb
... is a project to improve the understanding of the molecular basis of cancer through the application of genome analysis ... Available information includes annotations, data matrices, data reports, project metadata, and biospecimen metadata. ... including large-scale genome sequencing. TCGA offers a collection of APIs that provide REST-based, programmatic access to its ...https://www.programmableweb.com/api/cancer-genome-atlas/how-to
Genome project - Wikipedia
... molecular biology and bioinformatics have created the need for DNA annotation. DNA annotation or genome annotation is the ... private company involved in genome sequencing Knome, private company offering genome analysis & sequencing Pevsner, Jonathan ( ... Genome Project Domestic Cow Bovine Genome Honey Bee Genome Sequencing Consortium Horse genome Human microbiome project ... a complete genome sequence will involve 46 separate chromosome sequences. The Human Genome Project was a landmark genome ...https://en.wikipedia.org/wiki/Genome_project
Symbiose Project Team - INRIA/Irisa - Fabrice LEGEAI
Its main goals are to supply the needs on automatically or manually annotation, genome browsing or genome comparative analyses ... Ollivier M., Legeai F., Rispe C. (2010) Comparative analysis of the Acyrthosiphon pisum genome and expressed sequence tag-based ... A centralized bioinformatic resource for annotation of the pea aphid genome. Insect Molecular Biology vol19,0,5-12 ... Analysis of virion structural components reveals vestiges of the ancestral ichnovirus genome. PLoS Pathog. 2010 May 27;6(5). ...http://www.irisa.fr/symbiose/index2.php?option=com_content&task=view&id=70&pop=1&page=0
Frontiers | Genome-wide analysis of the CaHsp20 gene family in pepper: comprehensive sequence and expression profile analysis...
... were identified and renamed on the basis of their molecular weight, and then their gene structure, genome location, gene ... genome location, gene duplication, phylogenetic relationship and interaction network were also analyzed. The expression ... which provides the basis for further functional analyses of CaHsp20s in the formation of pepper acquired thermotoleance. ... were identified and renamed on the basis of their molecular weight, and then their gene structure, ...https://www.frontiersin.org/articles/10.3389/fpls.2015.00806/full
Project : USDA ARS
... four lines have been resequenced and the analysis of the sequences has been initiated. Knowledge of the genome sequence of ... Molecular, morphological and cytological analysis of diverse Brachypodium distachyon inbred lines. Genome. 52:876-890. ... Create a population of insertional mutants, sets of diverse inbred lines and improved annotation of the genome sequence. Apply ... Genome sequencing and analysis of the model grass Brachypodium distachyon. Nature. 463:763-768.. ...https://www.ars.usda.gov/research/project/?accnNo=418493&fy=2010
SH2D1B - Wikipedia
Eissmann P, Watzl C (2006). "Molecular analysis of NTB-A signaling: a role for EAT-2 in NTB-A-mediated activation of human NK ... 2006). "The DNA sequence and biological annotation of human chromosome 1". Nature. 441 (7091): 315-21. doi:10.1038/nature04727 ... 2004). "The Status, Quality, and Expansion of the NIH Full-Length cDNA Project: The Mammalian Gene Collection (MGC)". Genome ... 2003). "Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences". Proc. Natl. Acad. Sci ...https://en.wikipedia.org/wiki/SH2D1B
Genomics - Wikipedia
The DNA sequence assembly alone is of little value without additional analysis. Genome annotation is the process of attaching ... genomics is a field of molecular biology that attempts to make use of the vast wealth of data produced by genomic projects ( ... sequencing. Shotgun sequencing is a sequencing method designed for analysis of DNA sequences longer than 1000 base pairs, up to ... This project, completed in 2003, sequenced the entire genome for one specific person, and by 2007 this sequence was declared " ...https://en.wikipedia.org/wiki/Genomics
ERC2-IT1 Gene - GeneCards | ERC2-IT1 RNA Gene
The DNA sequence, annotation and analysis of human chromosome 3. (PMID: 16641997) Muzny DM … Gibbs RA (Nature 2006) 4 58 ... MGC Project Team (Genome research 2004) 4 58 ... Molecular cloning and expression analysis of five novel genes ... Molecular mass:. 14968 Da. Quaternary structure:. No Data Available SequenceCaution:. *Sequence=AAC39932.1; Type=Frameshift; ... Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. (PMID: 12477932) Strausberg RL ...https://www.genecards.org/cgi-bin/carddisp.pl?gene=ERC2-IT1
RPF1 Gene - GeneCards | RPF1 Protein | RPF1 Antibody
Genome research 2004) 3 4 58 * Functional proteomic analysis of human nucleolus. (PMID: 12429849) Scherl A … Diaz JJ (Molecular ... The DNA sequence and biological annotation of human chromosome 1. (PMID: 16710414) Gregory SG … Prigmore E (Nature 2006) 3 4 58 ... The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PMID: 15489334) ... Molecular mass:. 40111 Da. Quaternary structure:. No Data Available SequenceCaution:. *Sequence=CAH71915.1; Type=Erroneous gene ...http://www.genecards.org/cgi-bin/carddisp.pl?gene=RPF1
Palladin - Wikipedia
Sequencing and Analysis of 500 Novel Complete Protein Coding Human cDNAs". Genome Res. 11 (3): 422-35. doi:10.1101/gr.GR1547R. ... 2004). "Molecular analysis of the interaction between palladin and alpha-actinin". FEBS Lett. 566 (1-3): 30-4. doi:10.1016/j. ... 2005). "Generation and annotation of the DNA sequences of human chromosomes 2 and 4". Nature. 434 (7034): 724-31. doi:10.1038/ ... 2004). "The Status, Quality, and Expansion of the NIH Full-Length cDNA Project: The Mammalian Gene Collection (MGC)". Genome ...https://en.wikipedia.org/wiki/Palladin
Agmatinase - Wikipedia
Human AGMAT genome location and AGMAT gene details page in the UCSC Genome Browser. Molecular and Cellular Biology portal. ... 2006). "The DNA sequence and biological annotation of human chromosome 1". Nature. 441 (7091): 315-21. doi:10.1038/nature04727 ... 2003). "Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences". Proc. Natl. Acad. Sci ... 2004). "The Status, Quality, and Expansion of the NIH Full-Length cDNA Project: The Mammalian Gene Collection (MGC)". Genome ...https://en.wikipedia.org/wiki/Agmatinase
Genome-wide identification of rice class I metallothionein gene: tissue expression patterns and induction in response to heavy...
... are members of a family of cysteine-rich low molecular weight polypeptides which play an important role in heavy metal ... Our analysis suggests presence of 11 class I MT genes in rice genome (Release 7 of the MSU Rice Genome Annotation Project) ... Gene expression analysis by massively parallel signature sequencing (MPSS) on microbead arrays. Nat Biotechnol 18:630-634PubMed ... Zhou G, Xu Y, Li J, Yang L, Liu JY (2006) Molecular analyses of the metallothionein gene family in rice (Oryza sativa L.). J ...https://link.springer.com/article/10.1007/s10142-012-0297-9
C1orf35 Gene - GeneCards | MMTA2 Protein | MMTA2 Antibody
The DNA sequence and biological annotation of human chromosome 1. (PMID: 16710414) Gregory SG … Prigmore E (Nature 2006) 3 4 58 ... MGC Project Team (Genome research 2004) 3 4 58 ... Cloning and sequence analysis of tumor-associated gene hMMTAG2 ... No data available for Molecular function , Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Animal Models , Transcription ... Suggested Antigen Peptide Sequences for C1orf35 Gene. GenScript: Design optimal peptide antigens:. *Multiple myeloma tumor- ...https://www.genecards.org/cgi-bin/carddisp.pl?gene=C1orf35
Frontiers | Brassinosteroids Regulate OFP1, a DLT Interacting Protein, to Modulate Plant Architecture and Grain Morphology in...
Genetic analysis showed that the regulation of plant architecture by OFP1 depends on DLT function. In addition, we found OFP1 ... Genetic analysis showed that the regulation of plant architecture by OFP1 depends on DLT function. In addition, we found OFP1 ... According to rice genome annotation project2, OFP1 (LOC_Os01g12690) is intronless and contains 1185-bp coding sequence, 44-bp 5 ... Vector Constructions and Transgenic Analysis. The DNA sequence containing the promoter and coding sequence of OFP1 was cloned ...https://www.frontiersin.org/articles/10.3389/fpls.2017.01698/full
Map Position and Expression of the Genes in the 38 Region of Drosophila | Genetics
Sequence analysis: Our molecular work was based on P1 and bacterial artificial chromosome (BAC) genomic sequences produced by ... 1996 Around the genomes: the Drosophila genome project. Genome Res. 6: 71-79. ... additional sequence annotations were carried out to identify sequence similarities with those in the public domain. Each ... Biological information must now be extracted from the genome sequence by systematic functional analysis of genes. Computer ...http://www.genetics.org/content/158/4/1597
DUSP18 - Wikipedia
2005). "A genome annotation-driven approach to cloning the human ORFeome". Genome Biol. 5 (10): R84. doi:10.1186/gb-2004-5-10- ... 2003). "Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences". Proc. Natl. Acad. Sci ... 2004). "The Status, Quality, and Expansion of the NIH Full-Length cDNA Project: The Mammalian Gene Collection (MGC)". Genome ... 2003). "Molecular cloning and characterization of a novel dual-specificity phosphatase18 gene from human fetal brain". Biochim ...https://en.wikipedia.org/wiki/DUSP18
The Drosophila Gene taranis Encodes a Novel Trithorax Group Member Potentially Linked to the Cell Cycle Regulatory Apparatus |...
2001), analysis of the recently completed Drosophila genome sequence (Adamset al. 2000) allowed us to identify 10 other P ... The Drosophila protein and annotation databases were searched at the Berkeley Drosophila Genome Project (BDGP; http://www. ... The tara gene structure suggests a possible molecular mechanism of action. Our molecular analysis of the twin TARA proteins ... Sequence of the alternative tara mRNAs and proteins. The nucleotide sequence and deduced amino acid sequence for a putative ...http://www.genetics.org/content/160/2/547
MGI-Collaborators and Acknowledgements for Mouse Genome Informatics Projects
... and the Knockout Mouse Project (KOMP).. IMAGE Consortium (Integrated Molecular Analysis of Genomes and their Expression) and ... The miRBase Sequence Database contains all published miRNA sequences, genomic locations, and associated annotation.. Mouse ... The Genome Sequencing Center two-year project will produce expressed tag sequences (ESTs) from approximately 400,000 mouse ... We based the MGI Mouse Genome Browser, a tool for manipulating and displaying genome annotations, on JBrowse, a generic genome ...http://www.informatics.jax.org/mgihome/other/collab_and_acknow.shtml
Generation and analysis of expressed sequence tags (ESTs) for marker development in yam (Dioscorea alata L.) | BMC Genomics |...
Most of the current molecular markers for the yam genome by Mignouna et al. are based on AFLP and RAPD [14, 15]. However, for ... Sequence assembly, analysis and annotation. *a.. Preliminary sequencing data analysis: The Sanger sequences were analyzed using ... Mapman analysis: For data analysis by MapMan software version 3.5.0 BETA  http://gabi.rzpd.de/projects/MapMan/, the EST ... 454 sequence data analysis: The sequencing agency provided high quality raw reads as well as aligned EST sequences for three ...https://bmcgenomics.biomedcentral.com/articles/10.1186/1471-2164-12-100
IJMS | Free Full-Text | The MAPKKK Gene Family in Gossypium raimondii: Genome-Wide Identification, Classification and ...
Transcriptome sequencing data were used to investigate their transcript profiles in mature leaves, 0 day and 3 days post- ... for introns and additional domains were consistent with the evolutionary relationships inferred from the phylogenetic analysis ... In this study, we identified 78 putative MAPKKK genes in the genome of the diploid cotton, Gossypium raimondii. They were ... whereas Raf genes were distributed across the entire genome. Their conserved patterns observed ...http://www.mdpi.com/1422-0067/14/9/18740/htm
Prioritization and functional assessment of noncoding variants associated with complex diseases | SpringerLink
... and human genome resequencing projects (e.g., 1000 Genomes Project ), which provide a rich resource of genomic annotations ... Due to the population-scale sequencing feature of variants in the 1000 Genomes Project, the 1000 GENOMES part of the online ... A statistical framework to predict functional non-coding regions in the human genome through integrated analysis of annotation ... such as variants from 1000 Genomes, genomic annotations from ENCODE, and canonical pathways in the Molecular Signatures ...https://link.springer.com/article/10.1186%2Fs13073-018-0565-y
FlyBase - Wikipedia
... end sequencing project of cDNA clones from winged aphids. Similar large-scale expressed sequence tag (EST) sequencing projects ... GO annotation is useful for both small-scale and large-scale analyses. It can provide a first indication of the nature of a ... European Drosophila Genome Project) informatics groups. These groups recognized that most genome project and community data ... GO annotation comprises at least three components: a GO term that describes molecular function, biological role or subcellular ...https://en.wikipedia.org/wiki/FlyBase