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At least 1,261 records · Page 70Linked to original sources
PubMed1995

MMDB: an ASN.1 specification for macromolecular structure.

We present an exchange specification for data describing the three-dimensional structure of biological macromolecules. The specification was designed for MMDB, a Molecular Modeling Database supported by the National Center for Biotechnology Information (NCBI), based on information from the Protein Data Bank (PDB). In the MMDB specification, the chemical structures of molecules are described hierarchically as connectivity graphs, to directly support comparison by subgraph isomorphism or assignment algorithms. Three-dimensional coordinates are linked unambiguously to nodes in the chemical graph, so that homology-derived structures may be generated directly from alignment of chemically similar groups. In conversion to this form, data from PDB are extensively validated, so as to provide a description of chemical and spatial structure that is as accurate as possible. These changes in format and content of the known structure data are intended to support development of intelligent molecular modeling applications that make use of this invaluable information resource.

Amino Acid Sequence↗
PubMed2025

The Mycobacterium tuberculosis Transposon Sequencing Database (MtbTnDB): A Large-Scale Guide to Genetic Conditional Essentiality.

Characterizing genetic essentiality across various conditions is fundamental for understanding gene function. Transposon sequencing (TnSeq) is a powerful technique to generate genome-wide essentiality profiles in bacteria and has been extensively applied to Mycobacterium tuberculosis (Mtb). Dozens of TnSeq screens have yielded valuable insights into the biology of Mtb in vitro, inside macrophages, and in model host organisms. Despite their value, these Mtb TnSeq profiles have not been standardized or collated into a single, easily searchable database. This results in significant challenges when attempting to query and compare these resources, limiting our ability to obtain a comprehensive and consistent understanding of genetic conditional essentiality in Mtb. We address this problem by building a central repository of publicly available Mtb TnSeq screens, the Mtb transposon sequencing database (MtbTnDB). The MtbTnDB is a living resource that encompasses to date ≈150 standardized TnSeq screens, enabling open access to data, visualizations, and functional predictions through an interactive web app (www.mtbtndb.app). We conduct several statistical analyses on the complete database, such as demonstrating that (i) genes in the same genomic neighborhood have similar TnSeq profiles, and (ii) clusters of genes with similar TnSeq profiles are enriched for genes from similar functional categories. We further analyze the performance of machine learning models trained on TnSeq profiles to predict the functional annotation of orphan genes in Mtb. By facilitating the comparison of TnSeq screens across conditions, the MtbTnDB will accelerate the exploration of conditional genetic essentiality, provide insights into the functional organization of Mtb genes, and help predict gene function in this important human pathogen.

DNA Transposable Elements↗
PubMed2005

Successive maturation and senescence of individual leaves during barley whole plant ontogeny reveals temporal and spatial regulation of photosynthetic function in conjunction with C and N metabolism.

During ontogeny of barley plants (Hordeum vulgare, L. cv. Barke), a continuous developmental gradient of new leaves at the top and lower leaves undergoing senescence is maintained. In the course of senescence, specific recycling processes efficiently transfer valuable resources, e.g. nitrogen and carbon, to the growing young leaves and ears. In order to understand the temporal and spatial sequence of processes underlying this developmental program of leaf formation and degradation, changes in photosynthetic parameters, as well as C and N levels of all individual leaves were determined. During whole plant ontogeny, a strict sequential pattern of incorporation and degradation of C and N resources in the individual leaves, accompanied by a sequential loss of chlorophyll and photosynthetic function, was observed. In addition, protein levels of key enzymes of C and N anabolism AGPase (ADPglucose pyrophosphorylase) and GS (glutamine synthetase; plastidic isoform) also showed a strict pattern of sequential down-regulation in senescing leaves. Their decline preceded the breakdown of chlorophyll, total C and N levels and photosynthetic performance in the leaves. Quantitative real time PCR measurements revealed that the down-regulation of protein content of AGPase and GS correlated with a drastic decrease in their transcript levels. These data elucidated precise temporal and spatial regulation of C and N metabolism and allocation with photosynthetic function in the leaves during whole plant ontogeny of barley.

Base Sequence↗
PubMed2005

Marine genomics: a clearing-house for genomic and transcriptomic data of marine organisms.

BACKGROUND: The Marine Genomics project is a functional genomics initiative developed to provide a pipeline for the curation of Expressed Sequence Tags (ESTs) and gene expression microarray data for marine organisms. It provides a unique clearing-house for marine specific EST and microarray data and is currently available at http://www.marinegenomics.org. DESCRIPTION: The Marine Genomics pipeline automates the processing, maintenance, storage and analysis of EST and microarray data for an increasing number of marine species. It currently contains 19 species databases (over 46,000 EST sequences) that are maintained by registered users from local and remote locations in Europe and South America in addition to the USA. A collection of analysis tools are implemented. These include a pipeline upload tool for EST FASTA file, sequence trace file and microarray data, an annotative text search, automated sequence trimming, sequence quality control (QA/QC) editing, sequence BLAST capabilities and a tool for interactive submission to GenBank. Another feature of this resource is the integration with a scientific computing analysis environment implemented by MATLAB. CONCLUSION: The conglomeration of multiple marine organisms with integrated analysis tools enables users to focus on the comprehensive descriptions of transcriptomic responses to typical marine stresses. This cross species data comparison and integration enables users to contain their research within a marine-oriented data management and analysis environment.

Animals↗
PubMed2001

PlantsP: a functional genomics database for plant phosphorylation.

The PlantsP database is a curated database that combines information derived from sequences with experimental functional genomics information. PlantsP focuses on plant protein kinases and protein phosphatases. The database will specifically provide a resource for information on a collection of T-DNA insertion mutants (knockouts) in each protein kinase and phosphatase in Arabidopsis thaliana. PlantsP also provides a curated view of each protein that includes a comprehensive annotation of functionally related sequence motifs, sequence family definitions, alignments and phylogenetic trees, and descriptive information drawn directly from the literature. PlantsP is available at http://PlantsP.sdsc.edu.

Arabidopsis↗
PubMed2002

Expressed sequence tag analysis of human retina for the NEIBank Project: retbindin, an abundant, novel retinal cDNA and alternative splicing of other retina-preferred gene transcripts.

PURPOSE: Expressed sequence tag (EST) analysis was performed on un-normalized, unamplified cDNA libraries constructed from adult human retina to examine the expression profile of the tissue and to contribute resources for functional genomics studies. METHODS: Two size fractionated cDNA libraries (designated hd and he) were constructed from human retina RNA. Clones were randomly selected for sequencing and analyzed using the bioinformatics program GRIST (GRouping and Identification of Sequence Tags). PCR, Northern blotting and other techniques have been used to examine selected novel transcripts. RESULTS: After informatics analysis, 2200 retina cDNAs yield 1254 unique clusters, potentially representing individual genes. Opsin is the most abundant transcript and other retina transcripts are prominently represented. One abundant cluster of cDNAs encodes retbindin, a novel, retina preferred transcript which has sequence similarity to riboflavin binding proteins and whose gene is on chromosome 19. Variant transcripts of known retina genes are also observed, including an alternative exon in the coding sequence of the transcription factor NRL and a skipped coding sequence exon in the phosphodiesterase gammasubunit (PDE6G). CONCLUSIONS: The new retina cDNA libraries compare favorably in quality with those already represented in public databases. They are rich in retina specific sequences and include abundant cDNAs for a novel protein, retbindin. The function of retbindin remains to be determined, but it is a candidate for flavinoid or carotenoid binding. Analysis of multiple clones for highly expressed retina genes reveals several alternative splice variants in both coding and noncoding sequences which may have functional significance. The validated set of retina cDNAs will contribute to a nonredundant set for microarray construction.

Aged↗
PubMed2005

FAST DB: a website resource for the study of the expression regulation of human gene products.

Human genes use various mechanisms to generate different transcripts having different exon content, which in turn generate multiple protein isoforms having differential and even opposite biological activities. To understand the biological consequences of gene transcriptional activity modulation, it is necessary to integrate the capability of genes to generate distinct functional products, particularly because transcriptional stimuli also affect the exon content of their target gene products. For this purpose, we have developed a bioinformatics suite, FAST DB, which defines easily and accurately the exon content of all known transcripts produced by human genes. In addition, several tools have been developed, including a graphical presentation of all gene products, a sequence multi-alignment of all gene transcripts and an in silico PCR computer program. The FAST DB interface also offers extensive links to website resources for promoter analysis and transcription factor binding site prediction, splicing regulatory sequence prediction, as well as 5'- and 3'-untranslated region analysis. FAST DB has been designed to facilitate studies that integrate transcriptional and post-transcriptional events to investigate the expression regulation of human gene products.

Alternative Splicing↗
PubMed2000

The phytophthora genome initiative database: informatics and analysis for distributed pathogenomic research.

The Phytophthora Genome Initiative (PGI) is a distributed collaboration to study the genome and evolution of a particularly destructive group of plant pathogenic oomycete, with the goal of understanding the mechanisms of infection and resistance. NCGR provides informatics support for the collaboration as well as a centralized data repository. In the pilot phase of the project, several investigators prepared Phytophthora infestans and Phytophthora sojae EST and Phytophthora sojae BAC libraries and sent them to another laboratory for sequencing. Data from sequencing reactions were transferred to NCGR for analysis and curation. An analysis pipeline transforms raw data by performing simple analyses (i.e., vector removal and similarity searching) that are stored and can be retrieved by investigators using a web browser. Here we describe the database and access tools, provide an overview of the data therein and outline future plans. This resource has provided a unique opportunity for the distributed, collaborative study of a genus from which relatively little sequence data are available. Results may lead to insight into how better to control these pathogens. The homepage of PGI can be accessed at http:www.ncgr.org/pgi, with database access through the database access hyperlink.

Databases, Factual↗
PubMed1989

Time preference for health in cost-effectiveness analysis.

In program evaluation, should a predicted health status gain of 1 quality-adjusted life year (QALY) occurring 10 years from now be valued the same as a 1-QALY increase realizable 5 years from now? Or 1 year from now? If not, how should these future gains (or losses) be evaluated from a present-time perspective? Such questions arise frequently in cost-effectiveness analyses of disease prevention-health promotion programs. This report argues there are actually two distinct interpretations of time preference jointly relevant in many multiperiod program evaluations. 1) In ongoing programs where both present and future population cohorts are, in effect, vying for resources, decision makers must establish a relative social weighting of cohorts by specifying (now) the dollar worth of any unit QALY gain achievable in each. This is a problem of intergenerational equity in the resource allocation process. 2) Individuals, in any cohort, may possess a time preference for the sequence of events comprising their own multiperiod health outcomes. Current models, typically discounting future health gains to present value at some constant rate (r), can well accommodate the first interpretation but not (simultaneously) the second. In response, this report introduces a two-step evaluation procedure featuring the "scenario strategy," a holistic multiattribute preference approach to evaluating multiperiod health outcomes. It allows one to isolate statistically time preference effects at the individual or group level and to incorporate them naturally into the overall evaluation of multiperiod outcomes. A survey-based example and an appendix illustrate the main points.

Attitude to Health↗
PubMed2004

DomIns: a web resource for domain insertions in known protein structures.

Proteins can be formed by single or multiple domains. The process of recombination at the molecular level has generated a wide variety of multi-domain proteins with specific domain organization to cater to the functional requirements of an organism. The functional and structural costs of inserting a domain into another means that multi-domain proteins are usually formed by covalently linking the N-terminus of one domain to the C-terminus of the preceding domain. While this is true in a large proportion of multi-domain proteins, we find a significant fraction of proteins that are the result of domain insertion. The inserted domain breaks the sequence contiguity of the domain into which it is inserted leading to a novel domain organization. This web resource aims to document domain insertions in known protein structures that are classified in the SCOP database. The web server can be accessed from http://stash.mrc-lmb.cam. ac.uk/DomIns/.

Amino Acid Sequence↗
PubMed2004

AthaMap: an online resource for in silico transcription factor binding sites in the Arabidopsis thaliana genome.

Gene expression is controlled mainly by the binding of transcription factors to regulatory sequences. To generate a genomic map for regulatory sequences, the Arabidopsis thaliana genome was screened for putative transcription factor binding sites. Using publicly available data from the TRANSFAC database and from publications, alignment matrices for 23 transcription factors of 13 different factor families were used with the pattern search program Patser to determine the genomic positions of more than 2.4 x 10(6) putative binding sites. Due to the dense clustering of genes and the observation that regulatory sequences are not restricted to upstream regions, the prediction of binding sites was performed for the whole genome. The genomic positions and the underlying data were imported into the newly developed AthaMap database. This data can be accessed by positional information or the Arabidopsis Genome Initiative identification number. Putative binding sites are displayed in the defined region. Data on the matrices used and on the thresholds applied in these screens are given in the database. Considering the high density of sites it will be a valuable resource for generating models on gene expression regulation. The data are available at http://www.athamap.de.

Arabidopsis↗
PubMed1998

The major resistance gene cluster in lettuce is highly duplicated and spans several megabases.

At least 10 Dm genes conferring resistance to the oomycete downy mildew fungus Bremia lactucae map to the major resistance cluster in lettuce. We investigated the structure of this cluster in the lettuce cultivar Diana, which contains Dm3. A deletion breakpoint map of the chromosomal region flanking Dm3 was saturated with a variety of molecular markers. Several of these markers are components of a family of resistance gene candidates (RGC2) that encode a nucleotide binding site and a leucine-rich repeat region. These motifs are characteristic of plant disease resistance genes. Bacterial artificial chromosome clones were identified by using duplicated restriction fragment length polymorphism markers from the region, including the nucleotide binding site-encoding region of RGC2. Twenty-two distinct members of the RGC2 family were characterized from the bacterial artificial chromosomes; at least two additional family members exist. The RGC2 family is highly divergent; the nucleotide identity was as low as 53% between the most distantly related copies. These RGC2 genes span at least 3.5 Mb. Eighteen members were mapped on the deletion breakpoint map. A comparison between the phylogenetic and physical relationships of these sequences demonstrated that closely related copies are physically separated from one another and indicated that complex rearrangements have shaped this region. Analysis of low-copy genomic sequences detected no genes, including RGC2, in the Dm3 region, other than sequences related to retrotransposons and transposable elements. The related but divergent family of RGC2 genes may act as a resource for the generation of new resistance phenotypes through infrequent recombination or unequal crossing over.

Base Sequence↗
PubMed2000

Comparative DNA sequence analysis of genetic variation in the African grey parrot, Psittacus erythacus.

Comparative genome analysis promises to provide an insight into avian species that have been very little studied. To test the feasibility of this approach, we investigated the use of heterologous primers to generate single nucleotide polymorphisms (SNP) in the African grey parrot, Psittacus erythacus, using primers specific for chicken and turkey DNA fragments. Three of the primers were specific for three expressed sequence tagged sites in the turkey and the fourth for a chicken proteoglycan core protein-like DNA sequence. A total of about 2200 bp of the parrot genome was evaluated for DNA sequence variation. Seven SNPs were identified and confirmed by Mendelian segregation. The frequency distribution of the most common nucleotide at each SNP locus in an unrelated group of parrots ranged from 0.84 to 0.97. The percent similarity of each parrot sequence to the reference sequence was inconsistent and ranged from zero to 100%. The primers as well as the nucleotide variants described represent valuable resources for genetic analysis in the parrot.

Animals↗
PubMed2006

Genetic dissection of intermated recombinant inbred lines using a new genetic map of maize.

A new genetic map of maize, ISU-IBM Map4, that integrates 2029 existing markers with 1329 new indel polymorphism (IDP) markers has been developed using intermated recombinant inbred lines (IRILs) from the intermated B73xMo17 (IBM) population. The website http://magi.plantgenomics.iastate.edu provides access to IDP primer sequences, sequences from which IDP primers were designed, optimized marker-specific PCR conditions, and polymorphism data for all IDP markers. This new gene-based genetic map will facilitate a wide variety of genetic and genomic research projects, including map-based genome sequencing and gene cloning. The mosaic structures of the genomes of 91 IRILs, an important resource for identifying and mapping QTL and eQTL, were defined. Analyses of segregation data associated with markers genotyped in three B73/Mo17-derived mapping populations (F2, Syn5, and IBM) demonstrate that allele frequencies were significantly altered during the development of the IBM IRILs. The observations that two segregation distortion regions overlap with maize flowering-time QTL suggest that the altered allele frequencies were a consequence of inadvertent selection. Detection of two-locus gamete disequilibrium provides another means to extract functional genomic data from well-characterized plant RILs.

Alleles↗
PubMed2002

Mutational analysis of the central centromere targeting domain of human centromere protein C, (CENP-C).

Human centromere protein C (CENP-C) is an essential component of the inner kinetochore plate. A central region of CENP-C can bind DNA in vitro and is sufficient for targeting the protein to centromeres in vivo, raising the possibility that this domain mediates centromere localization via direct DNA binding. We performed a detailed molecular dissection of this domain to understand the mechanism by which CENP-C assembles at centromeres. By a combination of PCR mutagenesis and transient expression of GFP-tagged proteins in HeLa cells, we identified mutations that disrupt centromere localization of CENP-C in vivo. These cluster in a 12 amino acid region adjacent to the core domain required for in vitro DNA binding. This region is conserved between human and mouse, but is divergent or absent in invertebrate and plant CENP-C homologues. We suggest that these 12 amino acids are essential to confer specificity to DNA binding by CENP-C in vivo, or to mediate interaction with another as yet unidentified centromere component. A differential yeast two-hybrid screen failed to identify interactions specific to this sequence, but nonetheless identified 14 candidate proteins that interact with the central region of CENP-C. This collection of mutations and interacting proteins comprise a useful resource for further elucidating centromere assembly.

Amino Acid Sequence↗
PubMed2025

CancerTrialMatch: a computational resource for the management of biomarker-based clinical trials at a community cancer center.

MOTIVATION: The widespread implementation of next-generation sequencing in cancer care has enabled routine use of molecular and biomarker profiling. At our cancer center, as with many others, biomarker-based clinical trials are increasingly available to oncologists as potential treatment options via molecular tumor boards. To better support this effort, we developed CancerTrialMatch, a systematic approach to capture structured clinical trial data and match patients to trials based on their disease characteristics and sequencing profiles. RESULTS: CancerTrialMatch is an open-source application designed to streamline clinical trial curation and patient trial matching, while also enabling an institution's curated trial portfolio to be distributed across the institution for easy access to providers, care teams and researchers. It facilitates curating, updating, and searching for trials through a semi-automated interface built using R Shiny, MongoDB, and Docker. While much of the trial data is retrieved via the clinicaltrials.gov Application Programming Interface, certain items like biomarkers and disease subtypes are entered manually. The user inputs disease type using the OncoTree classification, and provides relevant biomarker details, such as mutations, copy numbers, fusions, and other disease-specific markers. This resource reduces the time required for institutional trial management and helps to identify potential clinical trials for patients, ultimately supporting larger clinical trial enrollment and enhancing the clinical application of precision oncology. AVAILABILITY AND IMPLEMENTATION: CancerTrialMatch was implemented and tested on Windows 11 (64-bit, 32 GB RAM) using WSL2 with Ubuntu 22.04. Docker 27.0.3 and Docker Compose 2.28.1 were used to build images and containers. Users can build it by cloning the repo and following the README instructions and supplemental file (cancertrialmatchsupplemental.pdf) . The source code and example data are available in GitHub and Figshare at https://github.com/AveraSD/CancerTrialMatch and 10.6084/m9.figshare.28447367 respectively.

Humans↗
PubMed1998

Evolutionary parameters of the transcribed mammalian genome: an analysis of 2,820 orthologous rodent and human sequences.

We have rigorously defined 2,820 orthologous mRNA and protein sequence pairs from rats, mice, and humans. Evolutionary rate analyses indicate that mammalian genes are evolving 17-30% more slowly than previous textbook values. Data are presented on the average properties of mRNA and protein sequences, on variations in sequence conservation in coding and noncoding regions, and on the absolute and relative frequencies of repetitive elements and splice sites in untranslated regions of mRNAs. Our data set contains 1,880 unique human/rodent sequence pairs that represent about 2-4% of all mammalian genes. Of the 1,880 human orthologs, 70% are present on a new gene map of the human genome, thus providing a valuable resource for cross-referencing human and rodent genomes. In addition to comparative mapping, these results have practical applications in the interpretation of noncoding sequence conservation between syntenic regions of human and mouse genomic sequence, and in the design and calibration of gene expression arrays.

Animals↗
PubMed2005

Meta-DP: domain prediction meta-server.

UNLABELLED: Meta-DP, a domain prediction meta-server provides a simple interface to predict domains in a given protein sequence using a number of domain prediction methods. The Meta-DP is a convenient resource because through accessing a single site, users automatically obtain the results of the various domain prediction methods along with a consensus prediction. The Meta-DP is currently coupled to 10 domain prediction servers and can be extended to include any number of methods. Meta-DP can thus become a centralized repository of available methods. Meta-DP was also used to evaluate the performance of 13 domain prediction methods in the context of CAFASP-DP. AVAILABILITY: The Meta-DP server is freely available at http://meta-dp.bioinformatics.buffalo.edu and the CAFASP-DP evaluation results are available at http://cafasp4.bioinformatics.buffalo.edu/dp/update.html CONTACT: hkaur@bioinformatics.buffalo.edu SUPPLEMENTARY INFORMATION: Available at http://cafasp4.bioinformatics.buffalo.edu/dp/update.html.

Algorithms↗