• metabolism
  • There were 689 significant differentially-expressed genes between the two libraries.GO annotation revealed that highly ranked genes were those implicated in small molecule metabolism, cellular component organisation or biogenesis at the cellular level and fatty acid metabolism.The expression patterns of 36 differentially expressed genes were confirmed by real-time (RT)-PCR. (nih.gov)
  • GO annotation revealed that highly ranked genes were those implicated in small molecule metabolism, cellular component organisation or biogenesis at the cellular level and fatty acid metabolism. (nih.gov)
  • rRNA sequences
  • D) For comparison, we show the tree derived from alignment of full length SSU rRNA sequences for twelve of the fourteen species included in the iPhy slices in parts (A), (B) and (C). For two of the species (Caenorhabditis sp. (nih.gov)
  • Plant
  • Plant Molecular Biology and Biotechnology Group, ARC Centre of Excellence for Integrative Legume Research, Melbourne School of Land and Environment, The University of Melbourne, Parkville, Victoria, Australia. (nih.gov)
  • The transcriptome of Utricularia vulgaris, a rootless plant with minimalist genome, reveals extreme alternative splicing and only moderate sequence similarity with Utricularia gibba. (nih.gov)
  • As shown in Fig. 2, the number of chromosomes in the selected diploid plant was confirmed to be 32 (n = 16) for sequencing purposes.Figure 2. (nih.gov)
  • Genome projects are scientific endeavours that ultimately aim to determine the complete genome sequence of an organism (be it an animal, a plant, a fungus, a bacterium, an archaean, a protist or a virus) and to annotate protein-coding genes and other important genome-encoded features. (wikipedia.org)
  • cDNA
  • We sequenced a normalized cDNA library prepared from total RNA extracted from shoots of U. vulgaris including leaves and traps, cultivated under sterile or outdoor conditions. (nih.gov)
  • Once RNA is extracted and purified from cells, it is sent to a high-throughput sequencing facility, where it is first reverse transcribed to create a cDNA library. (wikipedia.org)
  • This cDNA can then be fragmented into various lengths depending on the platform used for sequencing. (wikipedia.org)
  • The cDNA sequence reads are assembled into transcripts via a short read transcript assembly program. (wikipedia.org)
  • Homology
  • We have also identified, based in sequence homology searches, novel transcripts related to osmotic, drought, salinity and cold stress, senescence and early flowering. (nih.gov)
  • proteins
  • Among these proteins 27 had not been described before and 15 were identified in the newly sequenced species. (nih.gov)
  • The current increase in Gene Ontology (GO) annotations of proteins in the existing genome databases and their use in different analyses have fostered the improvement of several biomedical and biological applications. (nih.gov)
  • There are huge improvements in speed and in the variety of search modes, as well as the availability of additional data types, such as the display of annotation extensions and display of protein forms (splice variants and proteins with post translational modifications) (Figure 3). (nih.gov)
  • We present a new website that has been designed using a user-experience design process.We have introduced an annotation score for all entries in UniProt to represent the relative amount of knowledge known about each protein.These scores will be helpful in identifying which proteins are the best characterized and most informative for comparative analysis. (nih.gov)
  • Under the genetic code, these RNA strands are translated to specify the sequence of amino acids within proteins in a process called translation. (wikipedia.org)
  • This allows fine-grained functional diagnoses of uncharacterised sequences, allowing, for example, discrimination between family members on the basis of the ligands they bind or the proteins with which they interact, and highlighting potential oligomerisation or allosteric sites. (wikipedia.org)
  • Illumina
  • To investigate genes related to the pistil development of Japanese apricot, high-throughput sequencing technology (Illumina) was employed to survey gene expression profiles from perfect and imperfect Japanese apricot flower buds. (nih.gov)
  • Total RNA from I. paraguariensis was sequenced by Illumina HiSeq-2000 obtaining 72,031,388 pair-end 100 bp sequences. (nih.gov)
  • Each of the following platforms utilizes a different type of technology to sequence millions of short reads: 454 Sequencing, Illumina, and SOLiD. (wikipedia.org)
  • functional
  • DFLAT: functional annotation for human development. (nih.gov)
  • Functional analysis of expression data using the DFLAT annotation increases the number of implicated gene sets, reflecting the DFLAT's improved representation of current knowledge.Newly implicated significant gene sets also suggest specific hypotheses for future research.Overall, the DFLAT project contributes new functional annotation and gene sets likely to enhance our ability to interpret genomic studies of human fetal and neonatal development. (nih.gov)
  • The Gene Ontology (GO), a valuable and widely-used resource for characterizing gene function, offers perhaps the most suitable functional annotation system for this purpose. (nih.gov)
  • The Developmental FunctionaL Annotation at Tufts (DFLAT) project aims to improve the quality of analyses of fetal gene expression and regulation by curating human fetal gene functions using both manual and semi-automated GO procedures. (nih.gov)
  • Functional analysis of expression data using the DFLAT annotation increases the number of implicated gene sets, reflecting the DFLAT's improved representation of current knowledge. (nih.gov)
  • Overall, the DFLAT project contributes new functional annotation and gene sets likely to enhance our ability to interpret genomic studies of human fetal and neonatal development. (nih.gov)
  • Because several novel approaches performing better than the common BLAST tool are rarely applied in research, we hypothesized that there is a large gap between the number of known annotated enzymes and the actual number in the protein universe, which significantly limits our ability to extract additional biologically relevant functional information from the available sequencing data. (nih.gov)
  • Furthermore, our results highlight the necessity of using more advanced computational tools than BLAST in protein database annotations to extract additional biologically relevant functional information from the available biological sequences. (nih.gov)
  • To integrate this functional data into different analyses, several protein functional similarity measures based on GO term information content (IC) have been proposed and evaluated, especially in the context of annotation-based measures. (nih.gov)
  • He is interested in genome structural and functional annotation and applying it for rational design of biological systems. (wikipedia.org)
  • novel
  • A collection of gene sets (genes implicated in the same function or biological process), made by combining existing GO annotations with the 13,344 new DFLAT annotations, is available for use in novel analyses. (nih.gov)
  • To provide novel insights into the molecular basis of floral initiation, RNA-Seq was used to characterize the soybean transcriptome of leaf and micro-dissected shoot apical meristem at different time points after short-day treatment. (nih.gov)
  • citation needed] GeneDecks is a novel analysis tool to identify similar or partner genes, which provides a similarity metric by highlighting shared descriptors between genes, based on GeneCards' unique wealth of combinatorial annotations of human genes. (wikipedia.org)
  • As a result of the development of novel sequencing technologies, the years between 2008 and 2012 saw a large drop in the cost of sequencing. (wikipedia.org)
  • Chromosomes
  • Karyotype of A. hypochondriacus, the species selected for sequencing, showing diploidy with 32 chromosomes in mitotic root tips. (nih.gov)
  • For the human species, whose genome includes 22 pairs of autosomes and 2 sex chromosomes, a complete genome sequence will involve 46 separate chromosome sequences. (wikipedia.org)
  • Genome assembly refers to the process of taking a large number of short DNA sequences and putting them back together to create a representation of the original chromosomes from which the DNA originated. (wikipedia.org)
  • metadata
  • A special case is the Java programming language, where annotations can be used as a special form of syntactic metadata in the source code. (wikipedia.org)
  • In the digital imaging community the term annotation is commonly used for visible metadata superimposed on an image without changing the underlying master image, such as sticky notes, virtual laser pointers, circles, arrows, and black-outs (cf. redaction). (wikipedia.org)
  • similarity
  • Alignment-free approaches have been used in sequence similarity searches, clustering and classification of sequences, and more recently in phylogenetics (Figure 1). (wikipedia.org)
  • Inferred from Sequence Similarity (ISS) means a human curator has reviewed the output from a sequence similarity search and verified that it is biologically meaningful. (wikipedia.org)
  • Annotation unification of GeneDecks is based on the similarity in GeneCards gene-content space detection algorithms. (wikipedia.org)
  • orthologs
  • The right-hand side of the image depicts our procedure for deriving annotation from mouse orthologs. (nih.gov)
  • For those genes for which MGI has identified unique human orthologs, all mouse annotations with the required evidence codes are mapped to the corresponding human gene. (nih.gov)
  • Expression data of genes and miRNAs, annotation data like gene identifiers and GO terms, orthologs data and data of follow-up experiments are stored in the database. (nih.gov)
  • For the queried gene all the information stored in the database, i.e. tags, gene expression data, annotation data and orthologs data are listed. (nih.gov)
  • The search yields expression data, annotation data, orthologs, experimental data tags and favourite lists of the specified gene or miRNA (Figure 4). (nih.gov)
  • newly
  • Blinded literature review supports the validity of newly significant findings obtained with the DFLAT annotations. (nih.gov)
  • Analysis
  • We show how systematic biases can be addressed by using explicit criteria when selecting sequences for analysis from a large dataset. (nih.gov)
  • We first performed a promoter analysis with six PvC3Hs in Clade-XIV whose promoter sequences (−2.0 kb) were available in the switchgrass genome database (Figure 7). (nih.gov)
  • Multiple sequence analysis allowed us to predict that yerba mate contains ∼ 32,355 genes and 12,551 gene variants or isoforms. (nih.gov)
  • Combined QTL and selective sweep mappings with coding SNP annotation and cis-eQTL analysis revealed PARK2 and JAG2 as new candidate genes for adiposity regulation. (nih.gov)
  • The pioneering approaches for sequence analysis were based on sequence alignment either global or local, pairwise or multiple sequence alignment. (wikipedia.org)
  • A number of review articles provide in-depth review of alignment-free methods in sequence analysis. (wikipedia.org)
  • The comparison of the sequences from these genes are sometimes used in molecular analysis to construct phylogenetic trees, for example in Protists, Fungi, Insects, Tardigrades, and Vertebrates. (wikipedia.org)
  • As of 2016[update], there are more than 70 plug-ins available, providing for the visualization and analysis of gene expression, sequence, and structure data. (wikipedia.org)
  • Integration of gene and pathway annotation information from curated sources as well as through Gene Ontology enrichment analysis. (wikipedia.org)
  • Solovyev V.V. (1993) Fractal graphical representation and analysis of DNA and Protein sequences. (wikipedia.org)
  • UCSF Chimera (or simply Chimera) is an extensible program for interactive visualization and analysis of molecular structures and related data, including density maps, supramolecular assemblies, sequence alignments, docking results, trajectories, and conformational ensembles. (wikipedia.org)
  • data
  • Eligible annotations are then contributed to the GO database and included in GO releases of human data. (nih.gov)
  • Gene set analyses of expression in several data sets, including amniotic fluid RNA from fetuses with trisomies 21 and 18, umbilical cord blood, and blood from newborns with bronchopulmonary dysplasia, were conducted both with and without the DFLAT annotation. (nih.gov)
  • Eligible annotations are submitted to the Gene Ontology and included in subsequent data releases. (nih.gov)
  • The increasing availability of molecular sequence data means that the accuracy of future phylogenetic studies is likely to by limited by systematic bias and taxon choice rather than by data. (nih.gov)
  • Phylogenetic trees generated in external programs can be imported and stored, and iPhy integrates with iTol to allow trees to be displayed with rich data annotation. (nih.gov)
  • the difference between the two lies in data entry on the 'Annotation Extension' column, showing that the experiments were performed in different tissues, i.e. liver and skeletal muscle. (nih.gov)
  • Our study is the first comparison of two global sequence data sets in Utricularia. (nih.gov)
  • Among them sequence data is increasing at the exponential rate due to advent of next-generation sequencing technologies. (wikipedia.org)
  • Another limitation of alignment-based approaches is their computational complexity and are time-consuming and thus, are limited when dealing with large-scale sequence data. (wikipedia.org)
  • The advent of next-generation sequencing technologies has resulted in generation of voluminous sequencing data. (wikipedia.org)
  • The size of this sequence data poses challenges on alignment-based algorithms in their assembly, annotation and comparative studies. (wikipedia.org)
  • hydrolase activity, hydrolyzing O-glycosyl compounds Data source: Genome annotation is the practice of capturing data about a gene product, and GO annotations use terms from the GO ontology to do so. (wikipedia.org)
  • Annotation unification: Different data source often offer annotations with heterogeneous naming system. (wikipedia.org)
  • Visualization of gene expression (heatmaps, volcano plot), molecular interaction networks (through Cytoscape), protein sequence and protein structure data (e.g. (wikipedia.org)
  • Among data that can be shared between components are expression datasets, interaction networks, sample and marker (gene) sets and sequences. (wikipedia.org)
  • Its molecular structure was first identified by James Watson and Francis Crick at the Cavendish Laboratory within the University of Cambridge in 1953, whose model-building efforts were guided by X-ray diffraction data acquired by Raymond Gosling, who was a post-graduate student of Rosalind Franklin. (wikipedia.org)
  • An annotation is a metadatum (e.g. a post, explanation, markup) attached to location or other data. (wikipedia.org)
  • Often, annotations make book to a specific part of the new data. (wikipedia.org)
  • analyses
  • Taxonomic analyses of the coral holobiont disclosed the dominant presence of transcripts from coral (~70%) and Symbiodinium (~10-12%), as well as ~15-20% of unknown sequences which lacked sequence identity to known genes. (nih.gov)
  • Using new haplotype-based statistics exploiting the very high SNP density generated through whole-genome resequencing, we found 129 significant selective sweeps.We then focused on two of these QTL/sweeps.This study shows for the first time the interest of combining selective sweeps mapping, coding SNP annotation and cis-eQTL analyses for identifying causative genes for a complex trait, in the context of divergent lines selected for this specific trait. (nih.gov)
  • comparative
  • Recently, we found dramatic mitochondrial DNA divergence of Israeli Chamaeleo chamaeleon populations into two geographically distinct groups.We aimed to examine whether the same pattern of divergence could be found in nuclear genes.Our sequencing effort added a new resource for comparative genomic studies, and shed new light on the evolutionary dynamics of the OXPHOS system. (nih.gov)
  • Our sequencing effort added a new resource for comparative genomic studies, and shed new light on the evolutionary dynamics of the OXPHOS system. (nih.gov)
  • species
  • 5 and Ditylenchus africanus) no SSU rRNA sequence was available so we have included closely-related species (Caenorhabditis briggsae and Ditylenchus angustus). (nih.gov)
  • methods
  • The date and the creator of the annotation The evidence code comes from a controlled vocabulary of codes covering both manual and automated annotation methods. (wikipedia.org)
  • developed high-throughput sequencing (also called next-generation sequencing) technologies are both cost- and labor- effective, and the range of organisms studied via these methods is expanding. (wikipedia.org)
  • datasets
  • Here we present iPhy, a web application that lets non-technical users assemble, share and analyse DNA sequence datasets for multigene phylogenetic investigations. (nih.gov)
  • reliably
  • Alignment-based approaches generally give excellent results when the sequences under study are closely related and can be reliably aligned, but when the sequences are divergent, a reliable alignment cannot be obtained and hence the applications of sequence alignment are limited. (wikipedia.org)
  • Consortium
  • The members of the GO Consortium submit their annotation for integration and dissemination on the GO website, where they can be downloaded directly or viewed online using AmiGO. (wikipedia.org)
  • 1980s
  • Since the 1980s, sequence information has become increasingly abundant, many laboratories realized this and started to store these information in the central repositories- the primary database. (wikipedia.org)
  • reads
  • A genome assembly algorithm works by taking all the pieces and aligning them to one another, and detecting all places where two of the short sequences, or reads, overlap. (wikipedia.org)
  • Structural
  • Though genome alignment is a robust way of characterizing transcript sequences, this method is disadvantaged by its inability to account for incidents of structural alterations of mRNA transcripts, such as alternative splicing. (wikipedia.org)
  • alignment
  • A fingerprint is a group of conserved motifs taken from a multiple sequence alignment - together, the motifs form a characteristic signature for the aligned protein family. (wikipedia.org)
  • It "simultaneously displays structure, sequence, and alignment, and now has powerful annotation and alignment editing features", according to its official site. (wikipedia.org)
  • depicts
  • The NCBI GenBank lacks an EST database of yerba mate and depicts only 80 DNA sequences, mostly uncharacterized. (nih.gov)
  • Loci
  • Identification of agronomically important genes and/or loci is an important step for switchgrass molecular breeding. (nih.gov)