Genomes and Genes
nucleic acid databases
Summary: Databases containing information about NUCLEIC ACIDS such as BASE SEQUENCE; SNPS; NUCLEIC ACID CONFORMATION; and other properties. Information about the DNA fragments kept in a GENE LIBRARY or GENOMIC LIBRARY is often maintained in DNA databases.
- Caspi R, Altman T, Dale J, Dreher K, Fulcher C, Gilham F, et al. The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway/genome databases. Nucleic Acids Res. 2010;38:D473-9 pubmed publisher..The BioCyc PGDBs generated by SRI are offered for adoption by any party interested in curation of metabolic, regulatory, and genome-related information about an organism. ..
- . The Universal Protein Resource (UniProt) in 2010. Nucleic Acids Res. 2010;38:D142-8 pubmed publisher..UniProt is updated and distributed every 3 weeks and can be accessed online for searches or download at http://www.uniprot.org. ..
- Kim H, Murphy T, Xia J, Caragea D, Park Y, Beeman R, et al. BeetleBase in 2010: revisions to provide comprehensive genomic information for Tribolium castaneum. Nucleic Acids Res. 2010;38:D437-42 pubmed publisher..BeetleBase serves as a long-term repository for Tribolium genomic data, and is compatible with other model organism databases. ..
- Sinha R, Nikolajewa S, Szafranski K, Hiller M, Jahn N, Huse K, et al. Accurate prediction of NAGNAG alternative splicing. Nucleic Acids Res. 2009;37:3569-79 pubmed publisher..Our results suggest that the mechanism behind NAGNAG AS is simple, stochastic, and conserved among vertebrates and beyond. ..
- Cole J, Wang Q, Cardenas E, Fish J, Chai B, Farris R, et al. The Ribosomal Database Project: improved alignments and new tools for rRNA analysis. Nucleic Acids Res. 2009;37:D141-5 pubmed publisher..Details about RDP data and analytical functions can be found at http://rdp.cme.msu.edu/. ..
- Muller J, Szklarczyk D, Julien P, Letunic I, Roth A, Kuhn M, et al. eggNOG v2.0: extending the evolutionary genealogy of genes with enhanced non-supervised orthologous groups, species and functional annotations. Nucleic Acids Res. 2010;38:D190-5 pubmed publisher..Users can access the complete set of orthologous groups via a web interface at: http://eggnog.embl.de. ..
- Gould C, Diella F, Via A, Puntervoll P, Gemund C, Chabanis Davidson S, et al. ELM: the status of the 2010 eukaryotic linear motif resource. Nucleic Acids Res. 2010;38:D167-80 pubmed publisher..Using the links, researchers can explore the motifs, proteins, complex structures and associated literature to evaluate whether candidate motifs might be worth experimental investigation...
- Finn R, Mistry J, Tate J, Coggill P, Heger A, Pollington J, et al. The Pfam protein families database. Nucleic Acids Res. 2010;38:D211-22 pubmed publisher..Pfam is available via servers in the UK (http://pfam.sanger.ac.uk/), the USA (http://pfam.janelia.org/) and Sweden (http://pfam.sbc.su.se/). ..
- Parson W, Dür A. EMPOP--a forensic mtDNA database. Forensic Sci Int Genet. 2007;1:88-92 pubmed publisher..EMPOP has been launched on 16 October 2006 and is since then available at http://www.empop.org. ..
- Brooksbank C, Cameron G, Thornton J. The European Bioinformatics Institute's data resources. Nucleic Acids Res. 2010;38:D17-25 pubmed publisher..All of the resources described here can be accessed from the EMBL-EBI website: http://www.ebi.ac.uk. ..
- Contreras Moreira B. 3D-footprint: a database for the structural analysis of protein-DNA complexes. Nucleic Acids Res. 2010;38:D91-7 pubmed publisher..3D-footprint is available at http://floresta.eead.csic.es/3dfootprint with demo buttons and a comprehensive tutorial that illustrates the main uses of this resource. ..
- Dehal P, Joachimiak M, Price M, Bates J, Baumohl J, Chivian D, et al. MicrobesOnline: an integrated portal for comparative and functional genomics. Nucleic Acids Res. 2010;38:D396-400 pubmed publisher..Programmatic access to the database, along with source code and documentation, is available at http://microbesonline.org/programmers.html. ..
- Gardner P, Daub J, Tate J, Nawrocki E, Kolbe D, Lindgreen S, et al. Rfam: updates to the RNA families database. Nucleic Acids Res. 2009;37:D136-40 pubmed publisher..Recent improvements to the website, methodologies and data used by Rfam are discussed. Rfam is freely available on the Web at http://rfam.sanger.ac.uk/and http://rfam.janelia.org/. ..
- Benson D, Karsch Mizrachi I, Lipman D, Ostell J, Sayers E. GenBank. Nucleic Acids Res. 2010;38:D46-51 pubmed publisher..Complete bi-monthly releases and daily updates of the GenBank database are available by FTP. To access GenBank and its related retrieval and analysis services, begin at the NCBI homepage: www.ncbi.nlm.nih.gov. ..
- Qu W, Shen Z, Zhao D, Yang Y, Zhang C. MFEprimer: multiple factor evaluation of the specificity of PCR primers. Bioinformatics. 2009;25:276-8 pubmed publisher..Furthermore, we maintained a Primer3Plus server with a modified Primer3Manager for one-stop primer design and specificity checking. ..
- Davidsen T, Beck E, Ganapathy A, Montgomery R, Zafar N, Yang Q, et al. The comprehensive microbial resource. Nucleic Acids Res. 2010;38:D340-5 pubmed publisher..The code underlying the CMR website and the CMR database are freely available for download with no license restrictions. ..
- Klucar L, Stano M, Hajduk M. phiSITE: database of gene regulation in bacteriophages. Nucleic Acids Res. 2010;38:D366-70 pubmed publisher..The phiSITE is accessible at http://www.phisite.org/. ..
- Arnaud M, Chibucos M, Costanzo M, Crabtree J, Inglis D, Lotia A, et al. The Aspergillus Genome Database, a curated comparative genomics resource for gene, protein and sequence information for the Aspergillus research community. Nucleic Acids Res. 2010;38:D420-7 pubmed publisher..All of these data are freely available at http://www.aspgd.org. We welcome feedback from users and the research community at firstname.lastname@example.org...
- Dias Neto E, Nunes D, Giordano R, Sun J, Botz G, Yang K, et al. Next-generation phage display: integrating and comparing available molecular tools to enable cost-effective high-throughput analysis. PLoS ONE. 2009;4:e8338 pubmed publisher..Overall, qPhage plus pyrosequencing is superior to TU-counting plus Sanger sequencing and is proposed as the method of choice over a broad range of phage display applications in vitro, in cells, and in vivo. ..
- Spandidos A, Wang X, Wang H, Seed B. PrimerBank: a resource of human and mouse PCR primer pairs for gene expression detection and quantification. Nucleic Acids Res. 2010;38:D792-9 pubmed publisher..In all, 26,855 primer pairs covering most known mouse genes have been experimentally validated by QPCR, agarose gel analysis, sequencing and BLAST, and all validation data can be freely accessed from the PrimerBank web site. ..
- Forbes S, Tang G, Bindal N, Bamford S, Dawson E, Cole C, et al. COSMIC (the Catalogue of Somatic Mutations in Cancer): a resource to investigate acquired mutations in human cancer. Nucleic Acids Res. 2010;38:D652-7 pubmed publisher..Graphical views provide easily interpretable summaries of large quantities of data, and export functions can provide precise details of user-selected data. ..
- Kapushesky M, Emam I, Holloway E, Kurnosov P, Zorin A, Malone J, et al. Gene expression atlas at the European bioinformatics institute. Nucleic Acids Res. 2010;38:D690-8 pubmed publisher..Currently, the database contains information about more than 200,000 genes from nine species and almost 4500 biological conditions studied in over 30,000 assays from over 1000 independent studies. ..
- Wilkinson P, Sengerova J, Matteoni R, Chen C, Soulat G, Ureta Vidal A, et al. EMMA--mouse mutant resources for the international scientific community. Nucleic Acids Res. 2010;38:D570-6 pubmed publisher..g. Ensembl. Other resources are able to display EMMA data by accessing our Distributed Annotation System server. EMMA database access is publicly available at http://www.emmanet.org. ..
- Markowitz V, Chen I, Palaniappan K, Chu K, Szeto E, Grechkin Y, et al. The integrated microbial genomes system: an expanding comparative analysis resource. Nucleic Acids Res. 2010;38:D382-90 pubmed publisher..Several companion IMG systems have been set up in order to serve domain specific needs, such as expert review of genome annotations. IMG is available at http://img.jgi.doe.gov. ..
- Xiao F, Zuo Z, Cai G, Kang S, Gao X, Li T. miRecords: an integrated resource for microRNA-target interactions. Nucleic Acids Res. 2009;37:D105-10 pubmed publisher..The miRecords is available at http://miRecords.umn.edu/miRecords. ..
- Nawrocki E, Kolbe D, Eddy S. Infernal 1.0: inference of RNA alignments. Bioinformatics. 2009;25:1335-7 pubmed publisher..Source code, documentation and benchmark downloadable from http://infernal.janelia.org. INFERNAL is freely licensed under the GNU GPLv3 and should be portable to any POSIX-compliant operating system, including Linux and Mac OS/X. ..
- Chan P, Lowe T. GtRNAdb: a database of transfer RNA genes detected in genomic sequence. Nucleic Acids Res. 2009;37:D93-7 pubmed publisher..The database can be searched by primary sequence similarity, tRNA characteristics or phylogenetic group. The database is publicly available at http://gtrnadb.ucsc.edu. ..
- Schudoma C, May P, Nikiforova V, Walther D. Sequence-structure relationships in RNA loops: establishing the basis for loop homology modeling. Nucleic Acids Res. 2010;38:970-80 pubmed publisher..The loop-structure data sets are made available via an online database, RLooM. RLooM also offers functionalities for the modeling of RNA loop structures in support of RNA engineering and design efforts. ..
- Leinonen R, Akhtar R, Birney E, Bonfield J, Bower L, Corbett M, et al. Improvements to services at the European Nucleotide Archive. Nucleic Acids Res. 2010;38:D39-45 pubmed publisher..In this article, we briefly describe the content and scope of our archive and introduce major improvements to our services. ..
- Vizcaino J, Cote R, Reisinger F, Barsnes H, Foster J, Rameseder J, et al. The Proteomics Identifications database: 2010 update. Nucleic Acids Res. 2010;38:D736-42 pubmed publisher..Finally, we highlight the importance of data sharing in the proteomics field, and the corresponding integration of PRIDE with other databases in the ProteomExchange consortium. ..
- Kersey P, Lawson D, Birney E, Derwent P, Haimel M, Herrero J, et al. Ensembl Genomes: extending Ensembl across the taxonomic space. Nucleic Acids Res. 2010;38:D563-9 pubmed publisher..Additionally, extensive comparative analysis has been performed, both within defined clades and across the wider taxonomy, and sequence alignments and gene trees resulting from this can be accessed through the site. ..
- Yamazaki Y, Akashi R, Banno Y, Endo T, Ezura H, Fukami Kobayashi K, et al. NBRP databases: databases of biological resources in Japan. Nucleic Acids Res. 2010;38:D26-32 pubmed publisher..The results of searches provide links to online requests for distribution of research materials. A circulation system allows users to submit details of papers published on research conducted using NBRP resources. ..
- Grant D, Nelson R, Cannon S, Shoemaker R. SoyBase, the USDA-ARS soybean genetics and genomics database. Nucleic Acids Res. 2010;38:D843-6 pubmed publisher..SoyBase is the repository for controlled vocabularies for soybean growth, development and trait terms, which are also linked to the more general plant ontologies. SoyBase can be accessed at http://soybase.org. ..
- Sayers E, Barrett T, Benson D, Bolton E, Bryant S, Canese K, et al. Database resources of the National Center for Biotechnology Information. Nucleic Acids Res. 2010;38:D5-16 pubmed publisher..Augmenting many of the web applications are custom implementations of the BLAST program optimized to search specialized data sets. All these resources can be accessed through the NCBI home page at www.ncbi.nlm.nih.gov. ..
- Hyten D, Cannon S, Song Q, Weeks N, Fickus E, Shoemaker R, et al. High-throughput SNP discovery through deep resequencing of a reduced representation library to anchor and orient scaffolds in the soybean whole genome sequence. BMC Genomics. 2010;11:38 pubmed publisher..Those SNPs were then used to create a high resolution genetic map that assisted in the assembly of scaffolds from the 8x whole genome shotgun sequences into pseudomolecules corresponding to chromosomes of the organism. ..
- Kuhn R, Karolchik D, Zweig A, Wang T, Smith K, Rosenbloom K, et al. The UCSC Genome Browser Database: update 2009. Nucleic Acids Res. 2009;37:D755-61 pubmed publisher..A variety of other bioinformatics tools are also provided, including BLAT, the Table Browser, the Gene Sorter, the Proteome Browser, VisiGene and Genome Graphs. ..
- Price M, Dehal P, Arkin A. FastBLAST: homology relationships for millions of proteins. PLoS ONE. 2008;3:e3589 pubmed publisher..FastBLAST enables research groups that do not have supercomputers to analyze large protein sequence data sets. FastBLAST is open source software and is available at http://microbesonline.org/fastblast. ..
- Mihara M, Itoh T, Izawa T. In silico identification of short nucleotide sequences associated with gene expression of pollen development in rice. Plant Cell Physiol. 2008;49:1451-64 pubmed publisher..This approach should provide a general purpose algorithm for identifying short nucleotides associated with specific gene expression. ..
- Maselli V, di Bernardo D, Banfi S. CoGemiR: a comparative genomics microRNA database. BMC Genomics. 2008;9:457 pubmed publisher..For a more effective use of this data, we developed a user-friendly web interface that simply shows how a microRNA genomic context is related in different species. ..
- Benson D, Karsch Mizrachi I, Lipman D, Ostell J, Sayers E. GenBank. Nucleic Acids Res. 2009;37:D26-31 pubmed publisher..Complete bimonthly releases and daily updates of the GenBank database are available by FTP. To access GenBank and its related retrieval and analysis services, begin at the NCBI Homepage: www.ncbi.nlm.nih.gov. ..
- Sugawara H, Ikeo K, Fukuchi S, Gojobori T, Tateno Y. DDBJ dealing with mass data produced by the second generation sequencer. Nucleic Acids Res. 2009;37:D16-8 pubmed publisher..To cope with the current progress of sequencing technology, we also accepted and released more than 100 million of short reads of parasitic protozoa and their hosts that were produced by using a Solexa sequencer. ..
- Jiang Q, Wang Y, Hao Y, Juan L, Teng M, Zhang X, et al. miR2Disease: a manually curated database for microRNA deregulation in human disease. Nucleic Acids Res. 2009;37:D98-104 pubmed publisher..Once approved by the submission review committee, the submitted records will be included in the database. miR2Disease is freely available at http://www.miR2Disease.org. ..
- Lu M, Zhang Q, Deng M, Miao J, Guo Y, Gao W, et al. An analysis of human microRNA and disease associations. PLoS ONE. 2008;3:e3420 pubmed publisher..These findings can not only provide help in understanding the associations between microRNAs and human diseases but also suggest a new way to identify novel disease-associated microRNAs. ..
- Abraham M, Dror O, Nussinov R, Wolfson H. Analysis and classification of RNA tertiary structures. RNA. 2008;14:2274-89 pubmed publisher..Further study of these conserved substructures may suggest possible RNA domains and building blocks. This should be beneficial for structure prediction and for gaining insights into structure-function relationships. ..
- Xin Y, Olson W. BPS: a database of RNA base-pair structures. Nucleic Acids Res. 2009;37:D83-8 pubmed publisher..The BPS also includes an Atlas with representative images of the various base pairs, higher-order base interactions and isosteric pairs and links to statistical information about these groups of structures. ..
- Carver T, Berriman M, Tivey A, Patel C, Böhme U, Barrell B, et al. Artemis and ACT: viewing, annotating and comparing sequences stored in a relational database. Bioinformatics. 2008;24:2672-6 pubmed publisher..Artemis and ACT are freely available (under a GPL licence) for download (for MacOSX, UNIX and Windows) at the Wellcome Trust Sanger Institute web sites: http://www.sanger.ac.uk/Software/Artemis/ http://www.sanger.ac.uk/Software/ACT/ ..
- Yamaguchi Kabata Y, Shimada M, Hayakawa Y, Minoshima S, Chakraborty R, Gojobori T, et al. Distribution and effects of nonsense polymorphisms in human genes. PLoS ONE. 2008;3:e3393 pubmed publisher..These nonsense SNPs may include pathological variants that have not yet been reported. These data are available from Transcript View of H-InvDB and VarySysDB (http://h-invitational.jp/varygene/). ..
- Czerwoniec A, Dunin Horkawicz S, Purta E, Kaminska K, Kasprzak J, Bujnicki J, et al. MODOMICS: a database of RNA modification pathways. 2008 update. Nucleic Acids Res. 2009;37:D118-21 pubmed publisher..Many new options for database searching and querying have been included. MODOMICS can be accessed at http://genesilico.pl/modomics. ..
- Taccioli C, Fabbri E, Visone R, Volinia S, Calin G, Fong L, et al. UCbase & miRfunc: a database of ultraconserved sequences and microRNA function. Nucleic Acids Res. 2009;37:D41-8 pubmed publisher..The current release contains over 2000 sequences from three species (human, mouse and rat). As a web application, UCbase & miRfunc is platform independent and it is accessible at http://microrna.osu.edu/.UCbase4. ..
- Lefever S, Vandesompele J, Speleman F, Pattyn F. RTPrimerDB: the portal for real-time PCR primers and probes. Nucleic Acids Res. 2009;37:D942-5 pubmed publisher..RTPrimerDB is a one-stop portal for high-quality and highly annotated real-time PCR assays. ..
- Rouillard J, Gulari E. OligoArrayDb: pangenomic oligonucleotide microarray probe sets database. Nucleic Acids Res. 2009;37:D938-41 pubmed publisher..Probe sequences, in addition to a comprehensive set of annotations can be downloaded from this database. OligoArrayDb is publicly accessible online at http://berry.engin.umich.edu/oligoarraydb. ..
- Gong W, Ren Y, Zhou H, Wang Y, Kang S, Li T. siDRM: an effective and generally applicable online siRNA design tool. Bioinformatics. 2008;24:2405-6 pubmed publisher..A performance comparison using an independent dataset indicated that siDRM outperforms 19 existing siRNA design tools in identifying effective siRNAs. ..
- Markham N, Zuker M. UNAFold: software for nucleic acid folding and hybridization. Methods Mol Biol. 2008;453:3-31 pubmed publisher..Users are encouraged to create their own scripts to supplement what comes with the package. This evolving software is available for download at http://www.bioinfo.rpi.edu/applications/hybrid/download.php . ..
- Harris T, Antoshechkin I, Bieri T, Blasiar D, Chan J, Chen W, et al. WormBase: a comprehensive resource for nematode research. Nucleic Acids Res. 2010;38:D463-7 pubmed publisher..Here, we describe new species and data types now available at WormBase. In addition, we detail enhancements to our curatorial pipeline and website infrastructure to accommodate new genomes and an extensive user base. ..
- Lauc G, Dzijan S, Marjanovic D, Walsh S, Curran J, Buckleton J. Empirical support for the reliability of DNA interpretation in Croatia. Forensic Sci Int Genet. 2008;3:50-3 pubmed publisher..It is concluded that if consideration is given to relatedness and subpopulation effects the model of Balding and Nichols appears to give very good predictions. ..
- Alexiou P, Vergoulis T, Gleditzsch M, Prekas G, Dalamagas T, Megraw M, et al. miRGen 2.0: a database of microRNA genomic information and regulation. Nucleic Acids Res. 2010;38:D137-41 pubmed publisher..The miRGen database will be continuously maintained and freely available at http://www.microrna.gr/mirgen/. ..