Gene3D: structural assignments for the biologist and bioinformaticist alike

The Gene3D database (http://www.biochem.ucl.ac.uk/bsm/cath_new/Gene3D/) provides structural assignments for genes within complete genomes. These are available via the internet from either the World Wide Web or FTP. Assignments are made using PSI-BLAST and subsequently processed using the DRange protocol. The DRange protocol is an empirically benchmarked method for assessing the validity of structural assignments made using sequence searching methods where appropriate assignment statistics are collected and made available. Gene3D links assignments to their appropriate entries in relevent structural and classification resources (PDBsum, CATH database and the Dictionary of Homologous Superfamilies). Release 2.0 of Gene3D includes 62 genomes, 2 eukaryotes, 10 archaea and 40 bacteria. Currently, structural assignments can be made for between 30 and 40 percent of any given genome. In any genome, around half of those genes assigned a structural domain are assigned a single domain and the other half of the genes are assigned multiple structural domains. Gene3D is linked to the CATH database and is updated with each new update of CATH.     

Database on diagnosis of arthropod diseases in the Internet of the Julius Kühn‐Institute

A database on diagnosis of diseases of insects and other arthropods is available in a German and English version at http://arthropodenkrankheiten.jki.bund.de . It is based on 55 years of diagnostic investigations of living, diseased, or dead arthropods of about 450 species at the ‘Institute for Biological Control’ in Darmstadt, Germany. Results of 1951 accessions with several thousands of diagnosed specimens from 1953 to 2008 are presented. The diagnosed pathogens belong to six groups: viruses, bacteria including rickettsiae, fungi, microsporidia (recently assigned to fungi), protists, and nematodes. The database will be updated regularly.     

NMRShiftDB -- compound identification and structure elucidation support through a free community-built web database

Compound identification and support for computer-assisted structure elucidation via a free community-built web database for organic structures and their NMR data is described. The new database NMRShiftDB is available on . As the first NMR database, NMRShiftDB allows not only open access to the database but also open and peer reviewed submission of datasets, enabling the natural products community to build its first free repository of assigned 1H and 13C NMR spectra. In addition to the open access, the underlying database software is built solely from free software and is available under an open source license. This allows collaborating laboratories to fully replicate the database and to create a highly available network of NMRShiftDB mirrors. The database contains about 10,000 structures and assigned spectra, with new datasets constantly added. Its functionality includes (sub-) spectra and (sub-) structure searches as well as shift prediction of 13C spectra based on the current database material.     

Complete sequence of a new HLA-B35 allele found in a tribe of Mapuche Indians in the south of Argentina

The nucleotide sequence data reported in this paper have been submitted to the GenBank nucleotide sequence database and have been assigned the accession number U17107. The nameB*3509 was officially assigned by the WHO Nomenclature Committee in December 1994     

ArrayExpress--a public repository for microarray gene expression data at the EBI

ArrayExpress is a new public database of microarray gene expression data at the EBI, which is a generic gene expression database designed to hold data from all microarray platforms. ArrayExpress uses the annotation standard Minimum Information About a Microarray Experiment (MIAME) and the associated XML data exchange format Microarray Gene Expression Markup Language (MAGE-ML) and it is designed to store well annotated data in a structured way. The ArrayExpress infrastructure consists of the database itself, data submissions in MAGE-ML format or via an online submission tool MIAMExpress, online database query interface, and the Expression Profiler online analysis tool. ArrayExpress accepts three types of submission, arrays, experiments and protocols, each of these is assigned an accession number. Help on data submission and annotation is provided by the curation team. The database can be queried on parameters such as author, laboratory, organism, experiment or array types. With an increasing number of organisations adopting MAGE-ML standard, the volume of submissions to ArrayExpress is increasing rapidly. The database can be accessed at http://www.ebi.ac.uk/arrayexpress.     

The CCPN Metabolomics Project: a fast protocol for metabolite identification by 2D-NMR

SUMMARY: We present here the freely available Metabolomics Project resource specifically designed to work under the CcpNmr Analysis program produced by CCPN (Collaborative Computing Project for NMR) (Vranken et al., 2005, The CCPN data model for NMR spectroscopy: development of a software pipeline. Proteins, 59, 687-696). The project consists of a database of assigned 1D and 2D spectra of many common metabolites. The project aims to help the user to analyze and assign 1D and 2D NMR spectra of unknown metabolite mixtures. Spectra of unknown mixtures can be easily superimposed and compared with the database spectra, thus facilitating their assignment and identification. AVAILABILITY: The CCPN Metabolomics Project, together with an annotated example dataset, is freely available via: http://www.ccpn.ac.uk/metabolomics/.     

AvGI,an index of genes transcribed in the salivary glands of the ixodid tick Amblyomma variegatum

Random clones from a cDNA library made from mRNA purified from dissected salivary glands of feeding female Amblyomma variegatum ticks were subjected to single pass sequence analysis. A total of 3992 sequences with an average read length of 580 nucleotides have been used to construct a gene index called AvGI that consists of 2109 non-redundant sequences. A provisional gene identity has been assigned to 39% of the database entries by sequence similarity searches against a non-redundant amino acid database and a protein database that has been assigned gene ontology terms. Homologs of genes encoding basic cellular functions including previously characterised enzyme activities, such as stearoyl CoA saturase and protein phosphatase, of ixodid tick salivary glands were found. Several families of abundant cDNA sequences that may code for protein components of tick cement and A. variegatum proteins which may contribute to anti-haemostatic and anti-inflammatory responses, and, one with potential immunosuppressive activity, were also identified. Interference with the function of such proteins might disrupt the life cycle of A. variegatum and help to control this ectoparasite or to reduce its ability to transmit disease causing organisms. AvGI represents an electronic knowledge base, which can be used to launch investigations of the biology of the salivary glands of this tick species. The database may be accessed via the World Wide Web at http://www.tigr.org/tdb/tgi.shtml.     

Dynamic spectrum quality assessment and iterative computational analysis of shotgun proteomic data: toward more efficient identification of post-translational modifications, sequence polymorphisms, and novel peptides

In mass spectrometry-based proteomics, frequently hundreds of thousands of MS/MS spectra are collected in a single experiment. Of these, a relatively small fraction is confidently assigned to peptide sequences, whereas the majority of the spectra are not further analyzed. Spectra are not assigned to peptides for diverse reasons. These include deficiencies of the scoring schemes implemented in the database search tools, sequence variations (e.g. single nucleotide polymorphisms) or omissions in the database searched, post-translational or chemical modifications of the peptide analyzed, or the observation of sequences that are not anticipated from the genomic sequence (e.g. splice forms, somatic rearrangement, and processed proteins). To increase the amount of information that can be extracted from proteomic MS/MS datasets we developed a robust method that detects high quality spectra within the fraction of spectra unassigned by conventional sequence database searching and computes a quality score for each spectrum. We also demonstrate that iterative search strategies applied to such detected unassigned high quality spectra significantly increase the number of spectra that can be assigned from datasets and that biologically interesting new insights can be gained from existing data.     

GeneExpress: an integrator for databases and computer systems accessible by the Internet and intended for studying eukaryotic gene expression

We have developed GeneExpress that is the WWW-oriented integrator for the databases and systems supporting the investigation of gene expression. The total number of the Web-based resources integrated is 30. The database GeneNet on molecular events forming gene networks was assigned its integrative core. To navigate all these WWW-available resources, the SRS, HTML, and Java viewers were developed, http:@wwwmgs.bionet.nsc.ru/systems/GeneExpress/.     

Molecular cloning and characterization of horse DQB cDNA

The nucleotide sequence data reported in this paper have been submitted to the GenBank sequence database and have been assigned the accession number L33910     

Molecular cloning and expression of the mouse Tnf receptor type b

The nucleotide sequence data reported in this paper have been submitted to the EMBL nucleotide database and have been assigned the accession number X57796.     

Nucleotide sequences of an antiidiotypic antibody from a transplant recipient

The nucleotide sequence data reported in this paper have been submitted to the GenBank sequence database and have been assigned the accession number M99372.     

Molecular cloning of the dog homologue of the lymphocyte antigen CD28

The nucleotide data reported in this paper have been submitted to the GenBank nucleotide sequence database and have been assigned the accession number L22178.     

Sequence analysis of sheep T-cell receptor β chains

The nucleotide sequences reported in this paper have been submitted to the GenBank database and have been assigned the accession numbers M94181-M94183.     

Molecular cloning of the gene coding for pig α1→2fucosyltransferase

The nucleotide sequence data reported in this paper have been submitted to the GenBank nucleotide sequence database and have been assigned the accession number L50534     

The isolation and sequence of the chromosomal gene and regulatory regions of Ly-6A.2

The nucleotide sequence data reported in this paper have been submitted to the GenBank nucleotide sequence database and have been assigned the accession number M73552.     

An aberrantDRB4 null gene transcript is found that could encode a novel HLA-DR chain

The nucleotide sequence data reported in this paper have been submitted to the GenBank nucleotide sequence database and have been assigned the accession number M30694.