Assignment of taxonomic groups to uncultured bacterial clones from molecular nematode-associated bacteria clone libraries and the closest sequence match in database.

FULL-malaria is a database for a full-length-enriched cDNA library from the human malaria parasite Plasmodium falciparum. Because of its medical importance, this organism is the first target for genome sequencing of a eukaryotic pathogen; the sequences of two of its 14 chromosomes have already been determined. However, for the full exploitation of this rapidly accumulating information, correct identification of the genes and study of their expression are essential. Using the oligo-capping method, this database has produced a full-length-enriched cDNA library from erythrocytic stage parasites and performed one-pass reading. The database consists of nucleotide sequences of 2490 random clones that include 390 (16%) known malaria genes according to BLASTN analysis of the nr-nt database in GenBank; these represent 98 genes, and the clones for 48 of these genes contain the complete protein-coding sequence (49%). On the other hand, comparisons with the complete chromosome 2 sequence revealed that 35 of 210 predicted genes are expressed, and in addition led to detection of three new gene candidates that were not previously known. In total, 19 of these 38 clones (50%) were full-length. From these observations, it is expected that the database contains approximately 1000 genes, including 500 full-length clones. It should be an invaluable resource for the development of vaccines and novel drugs. Full-malaria has been updated in at least three points. (i) 8934 sequences generated from the addition of new libraries added so that the database collection of 11,424 full-length cDNAs covers 1375 (25%) of the estimated number of the entire 5409 parasite genes. (ii) All of its full-length cDNAs and GenBank EST sequences were mapped to genomic sequences together with publicly available annotated genes and other predictions. This precisely determined the gene structures and positions of the transcriptional start sites, which are indispensable for the identification of the promoter regions. (iii) A total of 4257 cDNA sequences were newly generated from murine malaria parasites, Plasmodium yoelii yoelii. The genome/cDNA sequences were compared at both nucleotide and amino acid levels, with those of P.falciparum, and the sequence alignment for each gene is presented graphically. This part of the database serves as a versatile platform to elucidate the function(s) of malaria genes by a comparative genomic approach. It should also be noted that all of the cDNAs represented in this database are supported by physical cDNA clones, which are publicly and freely available, and should serve as indispensable resources to explore functional analyses of malaria genomes. Sponsors: This database has been constructed and maintained by a Grant-in-Aid for Publication of Scientific Research Results from the Japan Society for the Promotion of Science (JSPS). This work was also supported by a Special Coordination Funds for Promoting Science and Technology from the Science and Technology Agency of Japan (STA) and a Grant-in-Aid for Scientific Research on Priority Areas from the Ministry of Education, Science, Sports and Culture of Japan.

Recent USDA/ARS patent- and PVP-protected plant cultivars that are available for licensing are described, including summary, contact, and patent number/status. Updated June 2018. Resources in this dataset:Resource Title: Available Plant Cultivars - June 2018. File Name: June Avail Plants.pptxResource Description: Slides presenting title, patent no./protection status, contact, docket number(s), description, and USPTO patent database URL of each new cultivar.Resource Title: Available Plant Cultivars - June 2018. File Name: Available_Plants_2018-06.csvResource Description: Listing of patent- and PVP-protected cultivars. This CSV file provides the title, patent no./protection status, contact, docket number(s), description, and USPTO patent database URL of each new cultivar. Machine-readable content extracted from corresponding slides accompanying this dataset.Resource Title: Available Plants Data Dictionary. File Name: available-plants-data-dictionary.csvResource Description: Defines fields, data type, allowed values etc. in available patented plants tables.

Database that integrates large-scale functional genomics assays and manual cDNA annotation with bioinformatics gene expression and protein analysis. LifeDB integrates data regarding full length cDNA clones and data on expression of encoded protein and their subcellular localization on mammalian cell line. LifeDB enables the scientific community to systematically search and select genes, proteins as well as cDNA of interest by specific database identifiers as well as gene name. It enables to visualize cDNA clone and subcellular location of proteins. It also links the results to external biological databases in order to provide a broader functional information. LifeDB also provides an annotation pipeline which facilitates an improved mapping of clones to known human reference transcripts from the RefSeq database and the Ensembl database. An advanced web interface enables the researchers to view the data in a more user friendly manner. Users can search using any one of the following search options available both in Search gene and cDNA clones and Search Sub-cellular locations of human proteins: By Keyword, By gene/transcript identifier, By plate name, By clone name, By cellular location. * The Search genes and cDNA clones results include: Gene Name, Ensemble ID, Genomic Region, Clone name, Plate name, Plate position, Classification class, Synonymous SNP''s, Non- synonymous SNP''s, Number of ambiguous positions, and Alignment with reference genes. * The Search sub-cellular locations of human proteins results include: Subcellular location, Gene Name, Ensemble ID, Clone name, True localization, Images, Start tag and End tag. Every result page has an option to download result data (excluding the microscopy images). On click of ''Download results as CSV-file'' link in the result page the user will be given a choice to open or save result data in form of a CSV (Comma Separated Values) file. Later the CSV file can be easily opened using Excel or OpenOffice.

Database of comparative gene mapping between species to assist the mapping of the genes related to phenotypic traits in livestock. The linkage maps, cytogenetic maps, polymerase chain reaction primers of pig, cattle, mouse and human, and their references have been included in the database, and the correspondence among species have been stipulated in the database. AGP is an animal genome database developed on a Unix workstation and maintained by a relational database management system. It is a joint project of National Institute of Agrobiological Sciences (NIAS) and Institute of the Society for Techno-innovation of Agriculture, Forestry and Fisheries (STAFF-Institute), under cooperation with other related research institutes. AGP also contains the Pig Expression Data Explorer (PEDE), a database of porcine EST collections derived from full-length cDNA libraries and full-length sequences of the cDNA clones picked from the EST collection. The EST sequences have been clustered and assembled, and their similarity to sequences in RefSeq, and UniGene determined. The PEDE database system was constructed to store sequences and similarity data of swine full-length cDNA libraries and to make them available to users. It provides interfaces for keyword and ID searches of BLAST results and enables users to obtain sequence data and names of clones of interest. Putative SNPs in EST assemblies have been classified according to breed specificity and their effect on coding amino acids, and the assemblies are equipped with an SNP search interface. The database contains porcine nucleotide sequences and cDNA clones that are ready for analyses such as expression in mammalian cells, because of their high likelihood of containing full-length CDS. PEDE will be useful for researchers who want to explore genes that may be responsible for traits such as disease susceptibility. The database also offers information regarding major and minor porcine-specific antigens, which might be investigated in regard to the use of pigs as models in various medical research applications.

The Human BAC Ends Database is a database of sequences from the ends of bacterial artificial chromosome (BAC) clones. A whole genome sequencing approach has been described in a map-as-you-go strategy. The complete sequence of a seed BAC is searched against a BAC end database and the minimally overlapping clones in each direction are selected for sequencing. As coverage increases, BAC end sequences provide samples for whole genome survey. It currently contains 743,000 end sequences from 470,000 clones (20 X clone coverage and 12% sequence coverage), generated by TIGR, UofWashington and CalTech, providing a sequence marker every 5 kb across the genome. The coverage by paired-ends on chromosome 22 is over 5X. The project is funded by DOE.

We analysed 2,800 programs in Java and C for which we knew they are functionally similar. We checked if existing clone detection tools are able to find these functional similarities and classified the non-detected differences. We make all used data, the analysis software as well as the resulting benchmark available here.

A greenhouse experiment was conducted to test the ability of the invasive clonal plant, Lepidium draba, to cope with damage to local and different ramets. The experiment was arranged in a fully factorial split-pot design that was blocked by bench position and provenance population of the plant. Plants were grown in 'split pots', where two adjoining pots were glued together with a small opening for a lateral root to pass through. A plant with a long lateral root was placed such that one ramet was in one pot, and a connected ramet was in the adjoining pot. One ramet was randomly assigned as the 'local' ramet and the other was assigned as the 'neighbor' ramet. Three treatments were applied in a fully factorial manner: (1) connection of lateral root (connected / not connected), (2) damage to local ramet by a generalist herbivore Trichoplusia ni (damaged / undamaged); (3) damage to the local ramet by a specialist herbivore Pieris rapae (damaged / undamaged). Measured responses w ...

Consensus sequencesConsensus sequences with assigned genotype for each individual. 48 text files in total - for each of the four lines, 10 daughter individual files (marked with "d") and files for two mother samples (marked with "m"). _consensus.txt file structure: contig 3'position coverage(sum) haplotype(X-OR-Y) diploid_homozygote(N)-OR-diploid_heterozygote(Y)-OR-haploid_low_coverage(L)-OR-hemizygote(H) consensus_sequenceMarkers_offspring_gntpsFour files - table of marker SNPs for each line and their genotype in each daughter. "_markers_offspring_gtps.txt" file structure: contig locus(3'position) base(SNP) mother.gtp d1 d2 d3 d4 d5 d6 d7 d8 d9 d10 "--"(same_as_mother_genotype) OR "LL"(Low_coverage) OR "NN"(missing genotype) OR different baseSanger_fasta_seqsFasta sequences of re-sequenced RAD-markers (Sanger sequencing). First line (">") denotes the sequenced individual and the primer used. "F" stands for forward and "R" for reverse primerLOH_analysis_pipelinePipeline summary inclu...

This dataset contains the predicted prices of the asset CLONES over the next 16 years. This data is calculated initially using a default 5 percent annual growth rate, and after page load, it features a sliding scale component where the user can then further adjust the growth rate to their own positive or negative projections. The maximum positive adjustable growth rate is 100 percent, and the minimum adjustable growth rate is -100 percent.

Database that integrates and disseminates the data from the cloning of complete set of predicted protein-encoding ORFs of Caenorhabditis elegans. It also allows the community to search for availability and quality of cloned ORFs. So far, ORF sequence tags (OSTs) obtained for all individual clones have allowed exon structure corrections for ORFs originally predicted by the C. elegans sequencing consortium. The database contains this OST information along with data pertinent to the cloning process.

This table contains daily elements measured at our synoptic station in Clones, Co Monaghan. The file is updated monthly. Values for each day include: Precipitation Amount (mm); Maximum Air Temperature (C); Minimum Air Temperature (C); 09utc Grass Minimum Temperature (C); Mean 10cm soil temperature (C); Mean CBL Pressure (hpa); Mean Wind Speed (kt); Highest ten minute mean wind speed (kt); Wind Direction at max 10 min mean (deg); Highest Gust (kt); Potential Evapotranspiration (mm); Evaporation (mm); Soil Moisture Deficits (mm); Global Radiation (J/cm sq.)

Database containing cDNA clone information of the brains of songbirds. These clones are annotated with behavioral information, as well as links to information of homologous genes of other species. The database includes over 91,000 zebra finch brain cDNAs (2009) sequenced by Duke, ESTIMA, and Rockefeller research groups. The project is a collaborative effort of the Jarvis Laboratory of Duke University, Duke Bioinformatics, and The Genomics group of RIKEN, with Erich D. Jarvis as P.I. and Kazuhiro Wada as Co-P.I. Microarrays with the cDNAs in this database are available at Duke http://mgm.duke.edu/genome/dna_micro/core/spotted.htm and through the NIH Neurosciences Microarray Consortium http://arrayconsortium.tgen.org/np2/public/overview.jsp

Brook trout clone filteredClone filtered VCF file of brook trout genotype data. VCF files were generated using stacks 2.46 with minimal filters (STACKS flags = -r 0.3, --min_maf 0.05). Data was generated using the SbfI enzyme, methods outlined in Ali et al. (2016)and prepared in the Genomic Variation Lab at the University of California--Davis and sequenced on Illumina NextSeq 500 (PE 75 bp reads, 96 samples/lane) at the Cornell Institute of Biotechnology.bt_CF.vcfBrook trout unfilteredNon-clone filtered (unfiltered) VCF file of brook trout genotype data. VCF files were generated using stacks 2.46 with minimal filters (STACKS flags = -r 0.3, --min_maf 0.05). Data was generated using the SbfI enzyme, methods outlined in Ali et al. (2016)and prepared in the Genomic Variation Lab at the University of California--Davis and sequenced on Illumina NextSeq 500 (PE 75 bp reads, 96 samples/lane) at the Cornell Institute of Biotechnologybt_noCF.vcfCisco clone filteredClone filtered (filtered) VCF f...

Code_for_the_main_modelCode for the main model in the paper. The ReadMe file is contained in the folder.Code_for_model_with_males_sexual_onlyCode for the model with males reproducing only sexually and females reproducing both sexually and asexually. The ReadMe file is contained in the folder.Code_for_relocation_of_sexual_seedsCode used to simulate the model with long-range dispersal of seeds instead of adults, or asexual fragments. The ReadMe file is contained in the folder.Data_for_Fig2Data used to generate Fig. 2.Data_for_Fig3Data used to generate Fig. 3.Data_for_Fig4Data used to generate Fig. 4.Data_for_Fig5Data used to generate Fig. 5.Data_for_Fig6Data used to generate Fig. 6.Data_for_Fig7Data used to generate Fig. 7.

Microbial community composition is inferred by a combination of automated ribosomal intergenic spacer analysis (ARISA) and PCR-generated clone library analysis. Clone libraries include both the 16S rRNA gene and the 16S-23S ribosomal intergenic spacer fragment. Phylogenetic assignments for individual ARISA fragments are obtained by comparing the ARISA fragment length from each clone to all of the profiles stored in our database. We have analyzed over 3900 clones obtained from 41 lakes that represent the range of trophic types found in temperate landscapes. Querying by taxonomic characteristics of the clone allows the user to retrieve clone IDs, sequence data, and characteristics of the sequence (length, chimera status, accession number, taxonomic affiliation). The data can be filtered by clone ID, ARISA fragment length (raw or binned), and/or taxonomic characteristics (Phylum and Phylum-Class). The output includes links to individual clone records, which contain more detailed information about how the clone was generated (researcher, library ID, project ID, primer sets used, etc.).

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 4,2023.The Human Gene and Protein Database presents SDS-PAGE patterns and other informations of human genes and proteins. The HGPD was constructed from full-length cDNAs. For conversion to Gateway entry clones, we first determined an open reading frame (ORF) region in each cDNA meeting the criteria. Those ORF regions were PCR-amplified utilizing selected resource cDNAs as templates. All the details of the construction and utilization of entry clones will be published elsewhere. Amino acid and nucleotide sequences of an ORF for each cDNA and sequence differences of Gateway entry clones from source cDNAs are presented in the GW: Gateway Summary window. Utilizing those clones with a very efficient cell-free protein synthesis system featuring wheat germ, we have produced a large number of human proteins in vitro. Expressed proteins were detected in almost all cases. Proteins in both total and supernatant fractions are shown in the PE: Protein Expression window. In addition, we have also successfully expressed proteins in HeLa cells and determined subcellular localizations of human proteins. These biological data are presented on the frame of cDNA clusters in the Human Gene and Protein Database. To build the basic frame of HGPD, sequences of FLJ full-length cDNAs and others deposited in public databases (Human ESTs, RefSeq, Ensembl, MGC, etc.) are assembled onto the genome sequences (NCBI Build 35 (UCSC hg17)). The majority of analysis data for cDNA sequences in HGPD are shared with the FLJ Human cDNA Database (http://flj.hinv.jp/) constructed as a human cDNA sequence analysis database focusing on mRNA varieties caused by variations in transcription start site (TSS) and splicing.

This table contains hourly elements for the last 30 years measured at our synoptic station in Clones, Co Monaghan. The file is updated monthly. Values for each hour may include (depending on the station): Precipitation Amount (mm); Air Temperature (°C); Wet Bulb Air Temperature (°C); Dew Point Air Temperature (°C); Vapour Pressure (hpa); Relative Humidity (%); Mean Sea Level Pressure (hPa); Mean Hourly Wind Speed (kt); Predominant Hourly wind Direction (kt); Synop Code Present Weather; Synop Code Past Weather; Sunshine duration (hours); Visibility (m); Cloud Ceiling Height (100s feet); Cloud Amount (octa).

The influence of plant species and aphid clone identity on the survivor number was analyzed separately for the three aphid races using generalized linear models with a quasipoisson error structure. The influence of plant species and clone identity on the average aphid weight was analyzed separately for the three aphid races using two-factorial ANOVA. P-values below significance level (P

This Dataset contains monthly elements measured at our synoptic station in Clones, Co Monaghan.The file is updated monthly. Values for each month including: Precipitation amount, Mean Air Temperature, Maximum Air Temperature (C), Minimum Air Temperature, Mean Maximum Temperature, Mean Minimum Temperature, Grass Minimum Temperature, Mean Wind Speed, Highest GUST, Sunshine duration.