IMIRS: a high-resolution 3D reconstruction package integrated with a relational image database

Recent advances in electron cryomicroscopy instrumentation and single particle reconstruction have created opportunities for high-throughput and high-resolution three-dimensional (3D) structure determination of macromolecular complexes. However, it has become impractical and inefficient to rely on conventional text file data management and command-line programs to organize and process the increasing numbers of image data required in high-resolution studies. Here, we present a distributed relational database for managing complex datasets and its integration into our high-resolution software package IMIRS (Image Management and Icosahedral Reconstruction System). IMIRS consists of a complete set of modular programs for icosahedral reconstruction organized under a graphical user interface and provides options for user-friendly, step-by-step data processing as well as automatic reconstruction. We show that the integration of data management with processing in IMIRS automates the tedious tasks of data management, enables data coherence, and facilitates information sharing in a distributed computer and user environment without significantly increasing the time of program execution. We demonstrate the applicability of IMIRS in icosahedral reconstruction toward high resolution by using it to obtain an 8-A 3D structure of an intermediate-sized dsRNA virus.     

cuticleDB: a relational database of Arthropod cuticular proteins

Background  

The insect exoskeleton or cuticle is a bi-partite composite of proteins and chitin that provides protective, skeletal and structural functions. Little information is available about the molecular structure of this important complex that exhibits a helicoidal architecture. Scores of sequences of cuticular proteins have been obtained from direct protein sequencing, from cDNAs, and from genomic analyses.     

IntergenicDB: a database for intergenic sequences

A whole genome contains not only coding regions, but also non-coding regions. These are located between the end of a given coding region and the beginning of the following coding region. For this reason, the information about gene regulation process underlies in intergenic regions. There is no easy way to obtain intergenic regions from current available databases. IntergenicDB was developed to integrate data of intergenic regions and their gene related information from NCBI databases. The main goal of INTERGENICDB is to offer friendly database for intergenic sequences of bacterial genomes.

Availability

http://intergenicdb.bioinfoucs.com/     

MIPDB: a relational database dedicated to MIP family proteins

BACKGROUND INFORMATION: The MIPs (major intrinsic proteins) constitute a large family of membrane proteins that facilitate the passive transport of water and small neutral solutes across cell membranes. Since water is the most abundant molecule in all living organisms, the discovery of selective water-transporting channels called AQPs (aquaporins) has led to new knowledge on both the physiological and molecular mechanisms of membrane permeability. The MIPs are identified in Archaea, Bacteria and Eukaryota, and the rapid accumulation of new sequences in the database provides an opportunity for large-scale analysis, to identify functional and/or structural signatures or to infer evolutionary relationships. To help perform such an analysis, we have developed MIPDB (database for MIP proteins), a relational database dedicated to members of the MIP family. RESULTS: MIPDB is a motif-oriented database that integrates data on 785 MIP proteins from more than 200 organisms and contains 230 distinct sequence motifs. MIPDB proposes the classification of MIP proteins into three functional subgroups: AQPs, glycerol-uptake facilitators and aquaglyceroporins. Plant MIPs are classified into three specific subgroups according to their subcellular distribution in the plasma membrane, tonoplast or the symbiosome membrane. Some motifs of the database are highly selective and can be used to predict the transport function or subcellular localization of unknown MIP proteins. CONCLUSIONS: MIPDB offers a user-friendly and intuitive interface for a rapid and easy access to MIP resources and to sequence analysis tools. MIPDB is a web application, publicly accessible at http://idefix.univ-rennes1.fr:8080/Prot/index.html.     

OGRe: a relational database for comparative analysis of mitochondrial genomes

Organellar Genome Retrieval (OGRe) is a relational database of complete mitochondrial genome sequences for over 250 Metazoan species. OGRe provides a resource for the comparative analysis of mitochondrial genomes at several levels. At the sequence level, OGRe allows the retrieval of any selected set of mitochondrial genes from any selected set of species. Species are classified using a taxonomic system that allows easy selection of related groups of species. Sequence alignments are also available for some species. At the level of individual nucleotides, the system contains information on base frequencies and codon usage frequencies that can be compared between organisms. At the level of whole genomes, OGRe provides several ways of visualizing information on gene order. Diagrams illustrating the genome arrangement can be generated for any selected set of species automatically from the information in the database. Searches can be done based on gene arrangement to find sets of species that have the same order as one another. Diagrams for pairwise comparison of species can be produced that show the positions of break-points in the gene order and use colour to highlight the sections of the genome that have moved. OGRe is available from http://www.bioinf.man.ac.uk/ogre.     

miSolRNA: A tomato micro RNA relational database

Background  

The economic importance of Solanaceae plant species is well documented and tomato has become a model for functional genomics studies. In plants, important processes are regulated by microRNAs (miRNA).     

The translational signal database, TransTerm, is now a relational database.

TransTerm-97 contains more than 97 500 non-redundant coding-sequence initiation and termination contexts compiled from GenBank, release 101 (15-June-1997). In addition, several coding sequence parameters are available: coding sequence length, Nc, GC3, and, when it is computable, codon adaptation index (CAI). Codon usage tables and summaries of start and stop codon contexts are also included. The information covers more than 325 species and organelles, including seven complete bacterial genomes and one complete eukaryotic genome. To promote research in translational control of protein synthesis, TransTerm has been converted into a relational database to ease the process of making queries. The relational database manager, Postgresql, gives access to the database using SQL (Structured Query Language). A World Wide Web interface using forms is being completed to allow the casual user access to the database. Extensions are planned to include the full 5'-UTR, full coding sequence and 3'-UTR. TransTerm-97 is available on the World Wide Web at:http://biochem. otago.ac.nz:800/Transterm/homepage.html     

MIPS: a database for genomes and protein sequences

The Munich Information Center for Protein Sequences (MIPS-GSF), Martinsried, near Munich, Germany, continues its longstanding tradition to develop and maintain high quality curated genome databases. In addition, efforts have been intensified to cover the wealth of complete genome sequences in a systematic, comprehensive form. Bioinformatics, supporting national as well as European sequencing and functional analysis projects, has resulted in several up-to-date genome-oriented databases. This report describes growing databases reflecting the progress of sequencing the Arabidopsis thaliana (MATDB) and Neurospora crassa genomes (MNCDB), the yeast genome database (MYGD) extended by functional analysis data, the database of annotated human EST-clusters (HIB) and the database of the complete cDNA sequences from the DHGP (German Human Genome Project). It also contains information on the up-to-date database of complete genomes (PEDANT), the classification of protein sequences (ProtFam) and the collection of protein sequence data within the framework of the PIR-International Protein Sequence Database. These databases can be accessed through the MIPS WWW server (http://www. mips.biochem.mpg.de).     

Tools for loading MEDLINE into a local relational database

Background  

Researchers who use MEDLINE for text mining, information extraction, or natural language processing may benefit from having a copy of MEDLINE that they can manage locally. The National Library of Medicine (NLM) distributes MEDLINE in eXtensible Markup Language (XML)-formatted text files, but it is difficult to query MEDLINE in that format. We have developed software tools to parse the MEDLINE data files and load their contents into a relational database. Although the task is conceptually straightforward, the size and scope of MEDLINE make the task nontrivial. Given the increasing importance of text analysis in biology and medicine, we believe a local installation of MEDLINE will provide helpful computing infrastructure for researchers.     

Processing of natural language queries to a relational database

MOTIVATION: A new method is developed to query a relational database in natural language (NL). RESULTS: The method, based on a semantic approach, interprets grammatical and lexical units of a natural language into concepts of subject domain, which are given in a conceptual scheme. The conceptual scheme is mapped formally onto the logical scheme. We applied the method to query the FlyEx database in natural language. FlyEx contains information on the expression of segmentation genes in Drosophila melanogaster. The method allows formulation of queries in various natural languages simultaneously, and is adaptive to changes in the knowledge domain and user's views. It provides optimal transformation of queries from natural language to SQL, as well as visualization of information as a hyperscheme. The method does not require specification of all possible language constructions as well as a standard grammar accuracy in formulation of NL queries.     

RADAR,a relational archaeobotanical database for advanced research

The structure of the Dutch Relational Archaeobotanical Database (RADAR) is presented. RADAR is a rather compact archaeobotanical database that is controlled centrally, but can be distributed to individual scientists. For this reason RADAR contains only the most important archaeobotanical data. For detailed archaeological, botanical and regional palaeoenvironmental information, links can be established with the national archaeological database (ARCHIS), the national botanical database (BBR) and the European Pollen Database (EPD). The software used for manipulation of the database is PARADOX for reasons of its highly visible nature, its control facilities for data entry and the ease of importing and exporting data from and to many other programs. The potential of the database is demonstrated with query examples.