• A method for efficient detection and rapid molecular identification of genes in Drosophila melanogaster. (kit.jp)
  • Number of all variants in coding genes, which were called and annotated by GATK HaplotypeCaller ( 32 ) and snpEff ( 33 ) with annotation information from DFAST ( 34 ). (cdc.gov)
  • In silico identification of Drosophila melanogaster genes encoding RNA polymerase subunits. (flybase.org)
  • Systematic identification of tRNA genes in Drosophila melanogaster. (flybase.org)
  • The current coverage is, however, sufficient for the Human Genome Project to enter a new phase, in which the entire sequence can be analyzed to identify genes, regulatory regions and other genomic elements and structures. (biomedcentral.com)
  • Sequence data of the revised genome annotation including several hundreds of novel transcripts, improved gene models and candidate genes for alternative splicing have been made accessible in a comprehensive database. (biomedcentral.com)
  • Annotation of the recently determined genome sequence of the major dengue vector, Aedes aegypti, reveals an abundance of detoxification genes. (unicamp.br)
  • Van Emden B, Ramos H, Panchanathan S, Newfeld S, Kumar S: FlyExpress: An image-matching web-tool for finding genes with overlapping patterns of expression in Drosophila embryos.2006. (crossref.org)
  • Two such genes in Drosophila encode the enzymes dopa decarboxylase (Ddc) and tyrosine hydroxylase (ple) . (sdbonline.org)
  • Sequencing the genomes of multiple, taxonomically diverse eukaryotes enables in-depth comparative-genomic analysis which is expected to help in reconstructing ancestral eukaryotic genomes and major events in eukaryotic evolution and in making functional predictions for currently uncharacterized conserved genes. (biomedcentral.com)
  • The KOG analysis reveals a conserved core of largely essential eukaryotic genes as well as major diversification and innovation associated with evolution of eukaryotic genomes. (biomedcentral.com)
  • To efficiently extract functional and evolutionary information from multiple genomes, rational classification of genes based on homologous relationships is indispensable. (biomedcentral.com)
  • At the same time, the metabolic phenotype was used for genome-wide association analysis to analyze its genetic model and identify genes related to metabolite synthesis and metabolic pathways. (biomedcentral.com)
  • Drosophila melanogaster (fruit fly) antisense RNA:CR31912 (Dmel_CR31912) sequence is a product of FBgn0051912, asRNA:CR31912 genes. (rnacentral.org)
  • Sequence finishing and mapping of Drosophila melanogaster heterochromatin. (genscript.com)
  • 5' upstream sequence from genome annotation release 4.1.1. (kit.jp)
  • It accepts sequence data in a variety of formats and a basic LTR annotation in GFF3format as input. (uni-hamburg.de)
  • As output, LTRdigest creates GFF3 and CSV annotations as well as FASTA sequence files for all detected features. (uni-hamburg.de)
  • The sequence of the human nuclear genome has been completed in draft form by an international public consortium consisting of 16 sequencing centers and associated computational facilities [ 1 ]. (biomedcentral.com)
  • As of late 2000, the public human sequence was primarily based on approximately 24,000 accessioned bacterial artificial chromosome (BAC) clones covering 97% of the euchromatic portion of the genome [ 6 ]. (biomedcentral.com)
  • Thirty percent of the genome is in finished form, including the entire sequence of chromosomes 21 and 22 [ 7 ]. (biomedcentral.com)
  • Recently, the consortium has distributed a working draft assembly of the entire genome that removes redundancies, orients sequence fragments and clearly indicates gaps arising from sequencing and assembly. (biomedcentral.com)
  • The assembly provides simplified descriptions of the genome, as disparate data sources such as GenBank and numerous expressed sequence tag (EST) and protein databases are unified. (biomedcentral.com)
  • Release of the drosophila sequence was in 2002 ( link ). (bcm.edu)
  • An annotated genomic sequence of the corn anthracnose fungus Colletotrichum graminicola has been published previously, but correct identification of gene models by means of automated gene annotation remains a challenge. (biomedcentral.com)
  • Comparative analysis of RNA-Seq data and the genome sequence did not provide evidence for RNA editing in C. graminicola . (biomedcentral.com)
  • The frequency of each k-mer can be calculated from the genome sequence reads. (biomedcentral.com)
  • A previously reported study, where the wild soybean Glycine soja was sequenced and compared to the Glycine max reference, found 2.5 megabases (Mb) of substituted sequences, 4.6 kilobases (kb) of indels, 32.4 Mb of deletions and 8.3 Mb of new sequences in a total of 915.5 Mb of genome sequence [ 14 ]. (genominfo.org)
  • This lncRNA sequence is 1,712 nucleotides long and is found in Drosophila melanogaster. (rnacentral.org)
  • No genome locations found for this sequence. (rnacentral.org)
  • In this work, we identified whole-genome and metagenomic operons via MetaRon (Metagenome and whole-genome opeRon prediction pipeline). (biomedcentral.com)
  • Starting from its application on whole-genome to simulated mixture of three whole-genomes ( E. coli MG1655, Mycobacterium tuberculosis H37Rv and Bacillus subtilis str. (biomedcentral.com)
  • MetaRon consistently achieved high operon prediction sensitivity, specificity and accuracy across E. coli whole-genome (97.8, 94.1 and 92.4%), simulated genome (93.7, 75.5 and 88.1%) and E. coli c20 (87, 91 and 88%,), respectively. (biomedcentral.com)
  • With MetaRon, we were able to remove two notable limitations of existing whole-genome operon prediction methods: (1) generalizability (ability to predict operons in unrelated bacterial genomes), and (2) whole-genome and metagenomic data management. (biomedcentral.com)
  • A total of 258.8 gigabases (Gb) of raw reads from whole-genome sequencing of the crab were generated by the Illumina HiSeq2000 platform. (biomedcentral.com)
  • We used the whole-genome shotgun sequencing strategy and constructed the subsequent short-insert libraries (170, 250, 500 and 800 bp) and long-insert libraries (2, 5, and 10 kb) using the standard protocol provided by Illumina (San Diego, USA). (biomedcentral.com)
  • Whole genome sequencing was carried out, and the DNA variations in the whole genome were compared between the normal and dwarf samples. (genominfo.org)
  • We found a large number of DNA variations in both the dwarf and semi-dwarf lines, with one single nucleotide polymorphism (SNP) per at least 3.68 kb in the dwarf lines and 1 SNP per 11.13 kb of the whole genome. (genominfo.org)
  • Although a great deal of information is available from whole genome sequencing, resequencing strategies have become an important tool to study allelic variations. (genominfo.org)
  • Term Matrix: A novel Gene Ontology annotation quality control system based on ontology term co-annotation patterns. (flybase.org)
  • Combined evidence annotation of transposable elements in genome sequences. (genscript.com)
  • LTR retrotransposons and endogenous retroviruses (ERVs) are transposable elements in eukaryotic genomes well suited for computational identification. (uni-hamburg.de)
  • Naturally occurring transposable elements disrupt hsp70 promoter function in Drosophila melanogaster. (nih.gov)
  • The FlyBase project is carried out by a consortium of Drosophila researchers and computer scientists at: Harvard University, University of Cambridge (UK), Indiana University and the University of New Mexico. (flybase.org)
  • FlyBase: updates to the Drosophila melanogaster knowledge base. (flybase.org)
  • In coordination with FlyBase, we are transitioning almost all of the RefSeq Drosophila assemblies to annotation produced primarily by NCBI's eukaryotic genome annotation pipeline . (nih.gov)
  • We'll continue to use the FlyBase annotation for Drosophila melanogaster (soon to be updated to Release 6.32), but we'll annotate the other species using available RNA-seq datasets and our latest software. (nih.gov)
  • Flybase BLAST -Searches all Drosophila reads and provides links to the individual matched sequences through the NCBI. (bcm.edu)
  • The recent draft assembly of the human genome provides a unified basis for describing genomic structure and function. (biomedcentral.com)
  • The Drosophila Genome Project was funded by the National Human Genome Research Institute , National Cancer Institute , and Howard Hughes Medical Institute . (bcm.edu)
  • Moreover, it would also be useful in the discovery of miRNAs in human genome and design of Dicer specific pre-miRNAs for potent gene silencing. (biomedcentral.com)
  • By integrating human protein-protein interaction networks and human genome-wide variations across populations, we described the differences between hubs and bottlenecks in this study. (biomedcentral.com)
  • Parsimonious scenarios of eukaryotic genome evolution and gene sets for ancestral eukaryotic forms were reconstructed. (biomedcentral.com)
  • Harmonizing model organism data in the Alliance of Genome Resources. (flybase.org)
  • Automated generation of gene summaries at the Alliance of Genome Resources. (flybase.org)
  • Alliance of Genome Resources Portal: unified model organism research platform. (flybase.org)
  • We now include 30 Drosophila species in the RefSeq dataset, with more planned. (nih.gov)
  • All RefSeq annotations are within the public domain. (nih.gov)
  • You can download these annotation data from the NCBI genomes FTP site or you can try the new NCBI Datasets tool. (nih.gov)
  • The snippet of the bash script above will create a "Reference" directory, download the genome of D. melanogaster in FASTA file, the corresponding GTF, and the protein sequences for Aedes aegypti . (readthedocs.io)
  • Complete annotations as well as the members and sequences of the 62 groups reported are available for download. (uni-hamburg.de)
  • Finally, we confirmed that the repeat sequences occupy approximately 50.4 % of the crab genome. (biomedcentral.com)
  • This tutorial will guide you through the task of configuring and running the whole Daijin pipeline on a Drosophila melanogaster dataset comprising two different samples, using one aligner (HISAT) and two assemblers (Stringtie and CLASS2) as chosen methods. (readthedocs.io)
  • This gene count represents an increase of 58% and 36% compared with the fruitfly, Drosophila melanogaster, and the malaria mosquito, Anopheles gambiae, respectively. (unicamp.br)
  • FlyPhoneDB: An integrated web-based resource for cell-cell communication prediction in Drosophila. (flybase.org)
  • Comparative validation of the D. melanogaster modENCODE transcriptome annotation. (bcm.edu)
  • Here we describe results from the modENCODE cis-regulatory annotation project. (duke.edu)
  • Genome Biology. (wikipedia.org)
  • Genome Biology 22(1): 212. (uni-bielefeld.de)
  • Genome Biology 2007, 8(7):R145. (crossref.org)
  • The results provide quantitative support for major trends of eukaryotic evolution noticed previously at the qualitative level and a basis for detailed reconstruction of evolution of eukaryotic genomes and biology of ancestral forms. (biomedcentral.com)
  • In Xenopus, zebrafish, and Drosophila the major activation of zygotic transcription occurs as the cell cycle lengthens and gastrulation begins, a developmental period referred to as the midblastula transition. (elifesciences.org)
  • This will allow us to provide consistent, high-quality annotations across the full spectrum of Drosophila species, and also rapidly provide annotations as new high-quality assemblies become available. (nih.gov)
  • Comparative analysis of genomes from distant species provides new insights into gene functions, genome evolution and phylogeny. (biomedcentral.com)
  • Unfortunately, since we don't quite know how to construct viable genomes of extinct species, much less grow the creatures themselves, we don't know whether the depiction of the science is right. (genomevisualization.com)
  • To better understand this control, we profiled translational efficiencies and poly(A)-tail lengths throughout Drosophila oocyte maturation and early embryonic development. (elifesciences.org)
  • The MZT marks the transfer of control of development from the mother to the zygote as maternal mRNAs are degraded, transcription from the zygotic genome begins, and embryonic development becomes dependent on zygotic gene products ( Tadros and Lipshitz, 2009 ). (elifesciences.org)
  • Ye J, Chen J, Li Q, Kumar S: Classification of Drosophila embryonic developmental stage range based on gene expression pattern images. (crossref.org)
  • Functional annotation of the genome is primarily hampered by the lack of a unified transcript index. (biomedcentral.com)
  • Of these, three miRNAs were differentially expressed miRNAs and 18 miRNAs involved in sexual differentiation as determined by functional analysis with GO annotation and KEGG pathway analysis. (peerj.com)
  • 16), E. coli c20 draft genome extracted from chicken gut and finally on 145 whole-metagenome data samples from human gut. (biomedcentral.com)
  • The draft is sufficiently accurate to provide useful annotation, enabling direct observations of previously inferred biological phenomena. (biomedcentral.com)
  • The assembled draft genome will provide a valuable resource for the study of essential developmental processes and genetic determination of important traits of the Chinese mitten crab, and also for investigating crustacean evolution. (biomedcentral.com)
  • Drosophila melanogaster ER membrane protein complex 8-9 (EMC8-9), mRNA. (genscript.com)
  • Of the original eleven published by the Drosophila 12 Genomes Consortium in 2007, updates for nine are finished and the remaining two are planned. (nih.gov)
  • Regulatory loci affecting metabolites were identified in a metabolome genome-wide association study (mGWAS). (biomedcentral.com)
  • Fine-grained annotation and classification of de novo predicted LTR retrotransposons. (uni-hamburg.de)
  • dblp: Search for 'The Drosophila melanogaster PeptideAtlas facilitates the use of peptide data for improved fly proteomics and genome annotation. (dblp.org)
  • Gene Model Annotations for Drosophila melanogaster: Impact of High-Throughput Data. (genscript.com)
  • The study of TE expression faces one main challenge: given their repetitive nature, the majority of TE-derived reads map to multiple regions of the genome and these multi-mapping reads are consequently discarded in standard RNA-seq data processing pipelines. (bioconductor.org)
  • Finally, these annotation data were synthesized to produce observations of gene density and number that accord well with historical estimates. (biomedcentral.com)
  • By special request, we're making orthology data relative to D. melanogaster available on the Gene FTP site , and plan to expose that data in our public pages in the future. (nih.gov)
  • We produced a map of the Drosophila melanogaster regulatory genome on the basis of more than 300 chromatin immunoprecipitation data sets for eight chromatin features, five histone deacetylases and thirty-eight site-specific transcription factors at different stages of development. (duke.edu)
  • Ten peaks were obtained in the C. glutamicum ATCC 14067 genome including two new peaks related to three operons (RS_01910-RS_01915, RS_15995, and RS_16000). (frontiersin.org)
  • Direct mapping of chromatin modification marks and transcriptional factor binding sites genome-wide has successfully identified specific subtypes of regulatory elements. (duke.edu)
  • We extracted clean reads of the short-insert libraries (500 or 800 bp) to estimate the crab genome size by k-mer frequency distribution analysis [ 1 ]. (biomedcentral.com)
  • To identify novel regulators of JNK-dependent cell death, this study performed a dominant-modifier screen in Drosophila and found that the Toll pathway participates in JNK-mediated cell death. (sdbonline.org)
  • This study provides the first genome-wide captures of the dynamics of in vivo AmtR binding events and the regulatory network they define. (frontiersin.org)
  • A cis-regulatory map of the Drosophila genome. (duke.edu)
  • however, comprehensive annotation of the regulatory genome remains a significant challenge. (duke.edu)
  • Single nucleotide polymorphisms (SNPs) are ubiquitous in genomes and have emerged as a marker of choice, especially in sequenced plants [ 15 , 16 ]. (genominfo.org)
  • There were 10,061 significant SNPs associated with 253 metabolites that were widely distributed across the entire chicken genome. (biomedcentral.com)
  • Traditional genome-wide association studies (GWAS) can identify SNPs associated with phenotypes but have limited ability to analyze the mechanisms underlying these phenotypes [ 15 , 16 ]. (biomedcentral.com)
  • Tissue specificity of cyclin B expression in D. melanogaster]. (nih.gov)
  • Genome-wide atlas of gene expression in the adult mouse brain. (crossref.org)
  • Kumar S, Jayaraman K, Panchanathan S, Gurunathan R, Marti-Subirana A, Newfeld SJ: BEST: a novel computational approach for comparing gene expression patterns from early stages of Drosophlia melanogaster develeopment. (crossref.org)
  • Ye J, Chen J, Janardan R, Kumar S: Developmental stage annotation of Drosophila gene expression pattern images via an entire solution path for LDA. (crossref.org)
  • Ji S, Sun L, Jin R, Kumar S, Ye J: Automated annotation of Drosophila gene expression patterns using a controlled vocabulary. (crossref.org)
  • The gene set of the last common ancestor of the crown group consists of 3,413 KOGs and largely includes proteins involved in genome replication and expression, and central metabolism. (biomedcentral.com)
  • We describe numerous global features of the genome and examine the relationship of various genetic maps with the assembly. (biomedcentral.com)
  • We report the first genome sequencing, assembly, and annotation of the Chinese mitten crab. (biomedcentral.com)
  • Final genome assembly of the Chinese mitten crab is 1.12 Gb in total length, which is about 67.5 % of the estimated genome size. (biomedcentral.com)
  • analyses gradually elucidated the perfected genome-scale metabolic map of C. glutamicum , expanding the scope of its application. (frontiersin.org)