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Nucleic acids research
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2011
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2011 v.39 no.suppl_1
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- Author:
- Gaudet, Pascale; Fey, Petra; Basu, Siddhartha; Bushmanova, Yulia A.; Dodson, Robert; Sheppard, Kerry A.; Just, Eric M.; Kibbe, Warren A.; Chisholm, Rex L.
- Source:
- Nucleic acids research 2011 v.39 no.suppl_1 pp. D620
- ISSN:
- 0305-1048
- Subject:
- Amoebozoa; Dictyostelium discoideum; models; expressed sequence tags; biomedical research; nucleic acids; databases
- Abstract:
- ... dictyBase (http://www.dictybase.org), the model organism database for Dictyostelium, aims to provide the broad biomedical research community with well integrated, high quality data and tools for Dictyostelium discoideum and related species. dictyBase houses the complete genome sequence, ESTs, and the entire body of literature relevant to DICTYOSTELIUM: This information is curated to provide accura ...
- Author:
- Stein, Amelie; Céol, Arnaud; Aloy, Patrick
- Source:
- Nucleic acids research 2011 v.39 no.suppl_1 pp. D718
- ISSN:
- 0305-1048
- Subject:
- Internet; databases; nucleic acids; peptides
- Abstract:
- ... The database of three-dimensional interacting domains (3did) is a collection of protein interactions for which high-resolution three-dimensional structures are known. 3did exploits the availability of structural data to provide molecular details on interactions between two globular domains as well as novel domain-peptide interactions, derived using a recently published method from our lab. The int ...
- Author:
- Luo, Qibin; Pagel, Philipp; Vilne, Baiba; Frishman, Dmitrij
- Source:
- Nucleic acids research 2011 v.39 no.suppl_1 pp. D724
- ISSN:
- 0305-1048
- Subject:
- algorithms; computer software; databases; mutation; nucleic acids; phylogeny; prediction
- Abstract:
- ... Domain Interaction MAp (DIMA, available at http://webclu.bio.wzw.tum.de/dima) is a database of predicted and known interactions between protein domains. It integrates 5807 structurally known interactions imported from the iPfam and 3did databases and 46 900 domain interactions predicted by four computational methods: domain phylogenetic profiling, domain pair exclusion algorithm correlated mutatio ...
- Author:
- Yellaboina, Sailu; Tasneem, Asba; Zaykin, Dmitri V.; Raghavachari, Balaji; Jothi, Raja
- Source:
- Nucleic acids research 2011 v.39 no.suppl_1 pp. D730
- ISSN:
- 0305-1048
- Subject:
- Internet; bioinformatics; data collection; information sources; nucleic acids; prediction; protein-protein interactions
- Abstract:
- ... DOMINE is a comprehensive collection of known and predicted domain-domain interactions (DDIs) compiled from 15 different sources. The updated DOMINE includes 2285 new domain-domain interactions (DDIs) inferred from experimentally characterized high-resolution three-dimensional structures, and about 3500 novel predictions by five computational approaches published over the last 3 years. These addit ...
- Author:
- Murali, Thilakam; Pacifico, Svetlana; Yu, Jingkai; Guest, Stephen; Roberts, George G. III.; Finley, Russell L. Jr.
- Source:
- Nucleic acids research 2011 v.39 no.suppl_1 pp. D736
- ISSN:
- 0305-1048
- Subject:
- Drosophila; RNA; databases; gene expression; genes; humans; models; protein-protein interactions; transcription (genetics); transcription factors
- Abstract:
- ... DroID (http://droidb.org/), the Drosophila Interactions Database, is a comprehensive public resource for Drosophila gene and protein interactions. DroID contains genetic interactions and experimentally detected protein-protein interactions curated from the literature and from external databases, and predicted protein interactions based on experiments in other species. Protein interactions are anno ...
- Author:
- Knox, Craig; Law, Vivian; Jewison, Timothy; Liu, Philip; Ly, Son; Frolkis, Alex; Pon, Allison; Banco, Kelly; Mak, Christine; Neveu, Vanessa; Djoumbou, Yannick; Eisner, Roman; Guo, An Chi; Wishart, David S.
- Source:
- Nucleic acids research 2011 v.39 no.suppl_1 pp. D1035
- ISSN:
- 0305-1048
- Subject:
- chemistry; databases; genes; metabolites; new drugs; nucleic acids; pharmacokinetics; prices; proteins
- Abstract:
- ... DrugBank (http://www.drugbank.ca) is a richly annotated database of drug and drug target information. It contains extensive data on the nomenclature, ontology, chemistry, structure, function, action, pharmacology, pharmacokinetics, metabolism and pharmaceutical properties of both small molecule and large molecule (biotech) drugs. It also contains comprehensive information on the target diseases, p ...
- Author:
- Keseler, Ingrid M.; Collado-Vides, Julio; Santos-Zavaleta, Alberto; Peralta-Gil, Martin; Gama-Castro, Socorro; Muñiz-Rascado, Luis; Bonavides-Martinez, César; Paley, Suzanne; Krummenacker, Markus; Altman, Tomer; Kaipa, Pallavi; Spaulding, Aaron; Pacheco, John; Latendresse, Mario; Fulcher, Carol; Sarker, Malabika; Shearer, Alexander G.; Mackie, Amanda; Paulsen, Ian; Gunsalus, Robert P.; Karp, Peter D.
- Source:
- Nucleic acids research 2011 v.39 no.suppl_1 pp. D583
- ISSN:
- 0305-1048
- Subject:
- Escherichia coli K12; Internet; computer software; databases; gene expression; models; nucleic acids; operon; signal transduction; transcription (genetics)
- Abstract:
- ... EcoCyc (http://EcoCyc.org) is a comprehensive model organism database for Escherichia coli K-12 MG1655. From the scientific literature, EcoCyc captures the functions of individual E. coli gene products; their regulation at the transcriptional, post-transcriptional and protein level; and their organization into operons, complexes and pathways. EcoCyc users can search and browse the information in m ...
- Author:
- Hsin, Kun-Yi; Morgan, Hugh P.; Shave, Steven R.; Hinton, Andrew C.; Taylor, Paul; Walkinshaw, Malcolm D.
- Source:
- Nucleic acids research 2011 v.39 no.suppl_1 pp. D1042
- ISSN:
- 0305-1048
- Subject:
- Internet; chemical elements; databases; ligands; nucleic acids; pharmacology
- Abstract:
- ... We present the relational database EDULISS (EDinburgh University Ligand Selection System), which stores structural, physicochemical and pharmacophoric properties of small molecules. The database comprises a collection of over 4 million commercially available compounds from 28 different suppliers. A user-friendly web-based interface for EDULISS (available at http://eduliss.bch.ed.ac.uk/) has been e ...
- Author:
- Jehl, Marc-André; Arnold, Roland; Rattei, Thomas
- Source:
- Nucleic acids research 2011 v.39 no.suppl_1 pp. D591
- ISSN:
- 0305-1048
- Subject:
- Internet; bacterial proteins; databases; genome; host-pathogen relationships; information retrieval; microsymbionts; nucleic acids; prediction; protein secretion; signal peptide; user interface; virulence
- Abstract:
- ... Protein secretion is a key virulence mechanism of pathogenic and symbiotic bacteria, which makes the investigation of secreted proteins ('effectors') crucial for understanding the molecular bacterium-host interactions. Effective (http://effectors.org) is a database of predicted bacterial secreted proteins, implementing two complementary prediction strategies for protein secretion: the identificati ...
- Author:
- Lawson, Catherine L.; Baker, Matthew L.; Best, Christoph; Bi, Chunxiao; Dougherty, Matthew; Feng, Powei; van Ginkel, Glen; Devkota, Batsal; Lagerstedt, Ingvar; Ludtke, Steven J.; Newman, Richard H.; Oldfield, Tom J.; Rees, Ian; Sahni, Gaurav; Sala, Raul; Velankar, Sameer; Warren, Joe; Westbrook, John D.; Henrick, Kim; Kleywegt, Gerard J.; Berman, Helen M.; Chiu, Wah
- Source:
- Nucleic acids research 2011 v.39 no.suppl_1 pp. D456
- ISSN:
- 0305-1048
- Subject:
- bioinformatics; cryo-electron microscopy; databases; image analysis; models; nucleic acids; Europe
- Abstract:
- ... Cryo-electron microscopy reconstruction methods are uniquely able to reveal structures of many important macromolecules and macromolecular complexes. EMDataBank.org, a joint effort of the Protein Data Bank in Europe (PDBe), the Research Collaboratory for Structural Bioinformatics (RCSB) and the National Center for Macromolecular Imaging (NCMI), is a global 'one-stop shop' resource for deposition a ...
- Author:
- Raney, Brian J.; Cline, Melissa S.; Rosenbloom, Kate R.; Dreszer, Timothy R.; Learned, Katrina; Barber, Galt P.; Meyer, Laurence R.; Sloan, Cricket A.; Malladi, Venkat S.; Roskin, Krishna M.; Suh, Bernard B.; Hinrichs, Angie S.; Clawson, Hiram; Zweig, Ann S.; Kirkup, Vanessa; Fujita, Pauline A.; Rhead, Brooke; Smith, Kayla E.; Pohl, Andy; Kuhn, Robert M.; Karolchik, Donna; Haussler, David; Kent, W. James
- Source:
- Nucleic acids research 2011 v.39 no.suppl_1 pp. D871
- ISSN:
- 0305-1048
- Subject:
- DNA; DNA methylation; Internet; RNA; RNA-binding proteins; chromatin; data collection; genome; histones; humans; sequence analysis
- Abstract:
- ... The ENCODE project is an international consortium with a goal of cataloguing all the functional elements in the human genome. The ENCODE Data Coordination Center (DCC) at the University of California, Santa Cruz serves as the central repository for ENCODE data. In this role, the DCC offers a collection of high-throughput, genome-wide data generated with technologies such as ChIP-Seq, RNA-Seq, DNA ...
52. Ensembl 2011
- Author:
- Flicek, Paul; Amode, M. Ridwan; Barrell, Daniel; Beal, Kathryn; Brent, Simon; Chen, Yuan; Clapham, Peter; Coates, Guy; Fairley, Susan; Fitzgerald, Stephen; Gordon, Leo; Hendrix, Maurice; Hourlier, Thibaut; Johnson, Nathan; Kähäri, Andreas; Keefe, Damian; Keenan, Stephen; Kinsella, Rhoda; Kokocinski, Felix; Kulesha, Eugene; Larsson, Pontus; Longden, Ian; McLaren, William; Overduin, Bert; Pritchard, Bethan; Riat, Harpreet Singh; Rios, Daniel; Ritchie, Graham R.S.; Ruffier, Magali; Schuster, Michael; Sobral, Daniel; Spudich, Giulietta; Tang, Y. Amy; Trevanion, Stephen; Vandrovcova, Jana; Vilella, Albert J.; White, Simon; Wilder, Steven P.; Zadissa, Amonida; Zamora, Jorge; Aken, Bronwen L.; Birney, Ewan; Cunningham, Fiona; Dunham, Ian; Durbin, Richard; Fernández-Suarez, Xosé M.; Herrero, Javier; Hubbard, Tim J.P.; Parker, Anne; Proctor, Glenn; Vogel, Jan; Searle, Stephen M.J.
- Source:
- Nucleic acids research 2011 v.39 no.suppl_1 pp. D800
- ISSN:
- 0305-1048
- Subject:
- Danio rerio; biomedical research; genes; humans; infrastructure; mice; nucleic acids; rats
- Abstract:
- ... The Ensembl project (http://www.ensembl.org) seeks to enable genomic science by providing high quality, integrated annotation on chordate and selected eukaryotic genomes within a consistent and accessible infrastructure. All supported species include comprehensive, evidence-based gene annotations and a selected set of genomes includes additional data focused on variation, comparative, evolutionary ...
- Author:
- Maglott, Donna; Ostell, Jim; Pruitt, Kim D.; Tatusova, Tatiana
- Source:
- Nucleic acids research 2011 v.39 no.suppl_1 pp. D52
- ISSN:
- 0305-1048
- Subject:
- sequence analysis; phenotype; gene ontology; models; genes; nucleic acids; National Center for Biotechnology Information
- Abstract:
- ... Entrez Gene (http://www.ncbi.nlm.nih.gov/gene) is National Center for Biotechnology Information (NCBI)'s database for gene-specific information. Entrez Gene maintains records from genomes which have been completely sequenced, which have an active research community to submit gene-specific information, or which are scheduled for intense sequence analysis. The content represents the integration of c ...
- Author:
- Cuff, Alison L.; Sillitoe, Ian; Lewis, Tony; Clegg, Andrew B.; Rentzsch, Robert; Furnham, Nicholas; Pellegrini-Calace, Marialuisa; Jones, David; Thornton, Janet; Orengo, Christine A.
- Source:
- Nucleic acids research 2011 v.39 no.suppl_1 pp. D420
- ISSN:
- 0305-1048
- Subject:
- Internet; catalysts; databases; genomics; nucleic acids; protein structure; topology; transmembrane proteins
- Abstract:
- ... CATH version 3.3 (class, architecture, topology, homology) contains 128 688 domains, 2386 homologous superfamilies and 1233 fold groups, and reflects a major focus on classifying structural genomics (SG) structures and transmembrane proteins, both of which are likely to add structural novelty to the database and therefore increase the coverage of protein fold space within CATH. For CATH version 3. ...
- Author:
- Wong, Philip; Walter, Mathias; Lee, Wanseon; Mannhaupt, Gertrud; Münsterkötter, Martin; Mewes, Hans-Werner; Adam, Gerhard; Güldener, Ulrich
- Source:
- Nucleic acids research 2011 v.39 no.suppl_1 pp. D637
- ISSN:
- 0305-1048
- Subject:
- Fusarium graminearum; barley; corn; databases; genes; loci; models; nucleic acids; nucleotide sequences; plant pathogens; prediction; wheat
- Abstract:
- ... The MIPS Fusarium graminearum Genome Database (FGDB) was established as a comprehensive genome database on one of the most devastating fungal plant pathogens of wheat, barley and maize. The current version of FGDB v3.1 provides information on the full manually revised gene set based on the Broad Institute assembly FG3 genome sequence. The results of gene prediction tools were integrated with the h ...
- Author:
- Georgitsi, Marianthi; Viennas, Emmanouil; Antoniou, Dimitris I.; Gkantouna, Vassiliki; van Baal, Sjozef; Petricoin, Emanuel F. III.; Poulas, Konstantinos; Tzimas, Giannis; Patrinos, George P.
- Source:
- Nucleic acids research 2011 v.39 no.suppl_1 pp. D926
- ISSN:
- 0305-1048
- Subject:
- funding; humans; enzymes; transporters; genetic variation; data collection; models; genetic disorders; gene frequency; genes; genomics; nucleic acids; computer software; proteomics; nationalities and ethnic groups; databases
- Abstract:
- ... Frequency of INherited Disorders database (FIND base; http://www.findbase.org) records frequencies of causative genetic variations worldwide. Database records include the population and ethnic group or geographical region, the disorder name and the related gene, accompanied by links to any related external resources and the genetic variation together with its frequency in that population. In addit ...
- Author:
- Zhu, Lihua Julie; Christensen, Ryan G.; Kazemian, Majid; Hull, Christopher J.; Enuameh, Metewo Selase; Basciotta, Matthew D.; Brasefield, Jessie A.; Zhu, Cong; Asriyan, Yuna; Lapointe, David S.; Sinha, Saurabh; Wolfe, Scot A.; Brodsky, Michael H.
- Source:
- Nucleic acids research 2011 v.39 no.suppl_1 pp. D111
- ISSN:
- 0305-1048
- Subject:
- DNA; Drosophila; binding sites; databases; genome; transcription (genetics); transcription factors
- Abstract:
- ... FlyFactorSurvey (http://pgfe.umassmed.edu/TFDBS/) is a database of DNA binding specificities for Drosophila transcription factors (TFs) primarily determined using the bacterial one-hybrid system. The database provides community access to over 400 recognition motifs and position weight matrices for over 200 TFs, including many unpublished motifs. Search tools and flat file downloads are provided to ...
- Author:
- Tuda, Josef; Mongan, Arthur E.; Tolba, Mohammed E.M.; Imada, Mihoko; Yamagishi, Junya; Xuan, Xuenan; Wakaguri, Hiroyuki; Sugano, Sumio; Sugimoto, Chihiro; Suzuki, Yutaka
- Source:
- Nucleic acids research 2011 v.39 no.suppl_1 pp. D625
- ISSN:
- 0305-1048
- Subject:
- Plasmodium falciparum; RNA; Toxoplasma gondii; complementary DNA; data collection; databases; expressed sequence tags; gene expression; host-parasite relationships; humans; monophyly; parasites; sequence analysis; transcriptome
- Abstract:
- ... Full-Parasites (http://fullmal.hgc.jp/) is a transcriptome database of apicomplexa parasites, which include Plasmodium and Toxoplasma species. The latest version of Full-Parasites contains a total of 105 786 EST sequences from 12 parasites, of which 5925 full-length cDNAs have been completely sequenced. Full-Parasites also contain more than 30 million transcription start sites (TSS) for Plasmodium ...
59. GenBank
- Author:
- Benson, Dennis A.; Karsch-Mizrachi, Ilene; Lipman, David J.; Ostell, James; Sayers, Eric W.
- Source:
- Nucleic acids research 2011 v.39 no.suppl_1 pp. D32
- ISSN:
- 0305-1048
- Subject:
- DNA; Internet; genetic databases; genome; nucleotide sequences; protein structure; sequence homology; taxonomy; Japan
- Abstract:
- ... GenBank® is a comprehensive database that contains publicly available nucleotide sequences for more than 380 000 organisms named at the genus level or lower, obtained primarily through submissions from individual laboratories and batch submissions from large-scale sequencing projects, including whole genome shotgun (WGS) and environmental sampling projects. Most submissions are made using the web- ...
- Author:
- Seal, Ruth L.; Gordon, Susan M.; Lush, Michael J.; Wright, Mathew W.; Bruford, Elspeth A.
- Source:
- Nucleic acids research 2011 v.39 no.suppl_1 pp. D514
- ISSN:
- 0305-1048
- Subject:
- Internet; databases; genes; humans; nucleic acids; phenotype; proteomics; statistics
- Abstract:
- ... The HUGO Gene Nomenclature Committee (HGNC) aims to assign a unique gene symbol and name to every human gene. The HGNC database currently contains almost 30 000 approved gene symbols, over 19 000 of which represent protein-coding genes. The public website, www.genenames.org, displays all approved nomenclature within Symbol Reports that contain data curated by HGNC editors and links to related geno ...