TransTerm, the translational signal database, extended to include full coding sequences and untranslated regions.

TransTerm is a database of mRNA sequences and parameters useful for detecting translational control signals in general. TransTerm-98 has been expanded beyond previous years to include full coding sequences and UTRs, while retaining the original small contexts about the coding sequence start- and stop-codons. The database contains more than 130 000 non-redundant coding sequences with associated untranslated regions (UTRs) from over 450 species. This includes the complete genomes of 12 prokaryotic and one eukaryotic organism. 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. TransTerm-98 has both a relational database form with a WWW interface and a flatfile format, also available by Internet browser. TransTerm is available at: http://biochem.otago.ac.nz:800/Transterm/homepage.h tml     

The translational signal database, TransTerm: more organisms, complete genomes.

TransTerm is a database of initiation and termination sequence contexts from more than 250 organisms listed in GenBank, including the four complete genomes:Haemophilus influenzae, Methanococcus jannaschii, Mycoplasma genitalium,and Saccharomyces cerevisiae. For the current release, more than 60 000 coding sequences were analysed. The tabulated data include initiation and termination contexts organised by species along with quantitative parameters about individual coding sequences (length, %GC, GC3, Nc and CAI). There are also tables of initiation- and termination-region nucleotide-frequencies, codon usage tables and summaries of stop signal usage. TransTerm is available on the World Wide Web at: http://biochem.otago.ac.nz:800/Transterm/homepage.h tml     

TransTerm: a database of translational signals.

The TransTerm database of sequence contexts of stop and start codons has been expanded to include approximately 50% more species than last year's release. It now contains 148 organisms and >39 500 coding sequences; it is now available on the World Wide Web. The database includes: (i) initiation and termination sequence contexts organized by species; (ii) summary parameters about the individual sequences (sequence length, GC%, GC3, Nc, CAI) in addition to tables of base frequencies for each species' stop and start codon sequence context; (iii) species codon usage tables; and (iv) summary tables of stop signal frequency.     

NRSub: a non-redundant database for Bacillus subtilis.

In the context of the international project aimed at sequencing the whole genome of Bacillus subtilis we have developed a non-redundant, fully annotated database of sequences from this organism. Starting from the B.subtilis sequences available in the EMBL, GenBank and DDBJ collections we have removed all encountered duplications and then added extra annotations to the sequences (e.g. accession numbers for the genes, locations on the genetic map, codon usage, etc.) We have also added cross-references to the EMBL, MEDLINE, SWISS-PROT and ENZYME data banks. The present system results from merging of the NRSub and SubtiList databases and the sequence contigs used in the two systems are identical. NRSub is distributed as a flatfile in EMBL format (which is supported by most sequence analysis software packages) and as an ACNUC database, while SubtiList is distributed as a relational database under 4th Dimension. It is possible to access the data through two dedicated World Wide Web servers located in France and Japan.     

The EMBL nucleotide sequence database.

The EMBL Nucleotide Sequence Database (http://www.ebi.ac.uk/embl. html ) constitutes Europe's primary nucleotide sequence resource. DNA and RNA sequences are directly submitted from researchers and genome sequencing groups and collected from the scientific literature and patent applications (Fig. 1). In collaboration with DDBJ and GenBank the database is produced, maintained and distributed at the European Bioinformatics Institute. Database releases are produced quarterly and are distributed on CD-ROM. EBI's network services allow access to the most up-to-date data collection via Internet and World Wide Web interface, providing database searching and sequence similarity facilities plus access to a large number of additional databases.     

SubtiList: the reference database for the Bacillus subtilis genome

SubtiList is the reference database dedicated to the genome of Bacillus subtilis 168, the paradigm of Gram-positive endospore-forming bacteria. Developed in the framework of the B.subtilis genome project, SubtiList provides a curated dataset of DNA and protein sequences, combined with the relevant annotations and functional assignments. Information about gene functions and products is continuously updated by linking relevant bibliographic references. Recently, sequence corrections arising from both systematic verifications and submissions by individual scientists were included in the reference genome sequence. SubtiList is based on a generic relational data schema and a World Wide Web interface developed for the handling of bacterial genomes, called GenoList. The World Wide Web interface was designed to allow users to easily browse through genome data and retrieve information according to common biological queries. SubtiList also provides more elaborate tools, such as pattern searching, which are tightly connected to the overall browsing system. SubtiList is accessible at http://genolist.pasteur.fr/SubtiList/. Similar bacterial databases are accessible at http://genolist.pasteur.fr/.     

The NRSub database: update 1997.

In the context of the international project aiming at sequencing the whole genome of Bacillus subtilis we have developed NRSub, a non-redundant database of sequences from this organism. Starting from the B.subtilis sequences available in the repository collections we have removed all encountered duplications, then we have added extra annotations to the sequences (e.g. accession numbers for the genes, locations on the genetic map, codon usage index). We have also added cross-references with EMBL/GenBank/DDBJ, MEDLINE, SWISS-PROT and ENZYME databases. NRSub is distributed through anonymous FTP as a text file in EMBL format and as an ACNUC database. It is also possible to access the database through two dedicated World Wide Web servers located in France (http://acnuc.univ-lyon1.fr/nrsub/nrsub.++ +html ) and in Japan (http://ddbjs4h.genes.nig.ac.jp/ ).     

The non-redundant Bacillus subtilis (NRSub) database: update 1998.

The non-redundant Bacillus subtilis database (NRSub) has been developed in the context of the sequencing project devoted to this bacterium. As this project has reached completion, the whole genome is now available as a single contig. Thanks to the ACNUC database management system and its associated retrieval system Query_win, each functional region of the genome can be accessed individually. Extra annotations have been added such as accession numbers for the genes, locations on the genetic map, codon adaptation index values, as well as cross-references with other collections. NRSub is distributed through anonymous FTP as a text file in EMBL format and as an ACNUC database. It is also possible to access NRSub through two dedicated World Wide Web servers located in France (http://acnuc. univ-lyon1.fr/nrsub/nrsub.html ) and in Japan (http://ddbjs4h.genes. nig.ac.jp/ ).     

A mutation spectra database for bacterial and mammalian genes: 1998.

This database consists of over 24 000 mutations in 18 viral, bacterial, yeast or mammalian genes. The data are grouped as sets of DNA base sequence changes or spectra caused by a particular mutagen under defined conditions. The spectra are available on the World Wide Web at http://info.med.yale.edu/mutbase/ in two formats; in text format that can be browsed on-line or downloaded for use with a text editor and in dBASEIII format for use, after downloading, by relational database programs or by spreadsheets. Researchers are encouraged to submit DNA sequence changes to a suitable mutation database such as ours. A data entry program, MUTSIN, can be retrieved from this site. MUTSIN diagrams each mutation on the computer screen and alerts the user to any discrepancies.     

Codon usage tabulated from the international DNA sequence databases.

Codon usage in 87 602 genes has been calculated using the nucleotide sequence data obtained from the GenBank Genetic Sequence Data Bank (Release 90.0; September 1995). The database is called the CUTG Database; the complete form of the database can be obtained by anonymous ftp from DDBJ and a part of the database, which lists the frequency of codon use in each organism, is made searchable through our World Wide Web server.     

The translational termination signal database (TransTerm) now also includes initiation contexts.

The TransTerm database of termination codon contexts has been extended to include sense codon usage, and initiation codon contexts. The database was constructed from 23,721 coding sequences from 93 organisms. The database contains: a) the sequence around the termination codon (-10, +10); b) the sequence around the initiation codon (-20, +10); c) the length, 'G+C%' of the third position of codons (GC3), the 'codon adaptation index' (CAI) and the 'effective number of codons' statistic (Nc); d) summary tables for each organism including total codon usage, stop codon and tetranucleotide stop-signal usage, and matrices tallying base frequencies at each position around the initiation and termination codons. The data are arranged to facilitate investigation of the relationships between the three phases of protein synthesis. The database is available electronically from EMBL.     

The fibril_one on-line database: mutations,experimental conditions,and trends associated with amyloid fibril formation

The association of amyloid fibril formation with a number of important diseases, and the extensive study of this process in vitro, has resulted in a large literature containing a vast amount of information about the fibril formation process. This includes mutations and experimental conditions that promote or protect against fibril formation. A database (fibril_one) was designed to hold information relating to the formation of fibrils. It was populated by extensive searches of the literature and other databases. A powerful World Wide Web query interface to the database was developed, enabling a simple and effective method to view amyloidogenic mutations associated with specific proteins. The Web interface was used to identify trends in the data. This revealed that mutations promoting fibril formation through altered folding tend to be associated with destabilization of the native fold. In particular, tendencies of mutations to disrupt the native secondary structure and packing in the hydrophobic core were discovered to be significant. Query access to the database is available freely on the World Wide Web at http://www.bioinformatics.leeds.ac.uk/group/online/fibril_one.     

LGICdb: the ligand-gated ion channel database

Ligand-Gated Ion Channels (LGIC) are polymeric transmembrane proteins involved in the fast response to numerous neurotransmitters. All these receptors are formed by homologous subunits and the last two decades revealed an unexpected wealth of genes coding for these subunits. The Ligand-Gated Ion Channel database (LGICdb) has been developed to handle this increasing amount of data. The database aims to provide only one entry for each gene, containing annotated nucleic acid and protein sequences. The repository is carefully structured and the entries can be retrieved by various criteria. In addition to the sequences, the LGICdb provides multiple sequence alignments, phylogenetic analyses and atomic coordinates when available. The database is accessible via the World Wide Web (http://www.pasteur.fr/recherche/banques/LGIC /LGIC.html), where it is continuously updated. The version 16 (September 2000) available for download contained 333 entries covering 34 species.     

MRD: a microsatellite repeats database for prokaryotic and eukaryotic genomes

MRD is a database system to access the microsatellite repeats information of genomes such as archea, eubacteria, and other eukaryotic genomes whose sequence information is available in public domains. MRD stores information about simple tandemly repeated k-mer sequences where k= 1 to 6, i.e. monomer to hexamer. The web interface allows the users to search for the repeat of their interest and to know about the association of the repeat with genes and genomic regions in the specific organism. The data contains the abundance and distribution of microsatellites in the coding and non-coding regions of the genome. The exact location of repeats with respect to genomic regions of interest (such as UTR, exon, intron or intergenic regions) whichever is applicable to organism is highlighted. MRD is available on the World Wide Web at and/or . The database is designed as an open-ended system to accommodate the microsatellite repeats information of other genomes whose complete sequences will be available in future through public domain.     

The viroid and viroid-like RNA database.

The viroid and viroid-like RNA database is a compilation of all natural sequences published in journals or available from the GenBank and EMBL nucleotide sequence libraries. Several information regarding these RNA species such as the position of their self-catalytic domains and the open reading frame of the human hepatitits delta virus are provided. The database also includes a determination of the likely ancestral sequence of most species and a prediction of the most stable secondary structures of these sequences. This online database is available on the World Wide Web (http://www.callisto.si.usherb.ca/[symbol: see text]jpperra ). It should provide an excellent reference point for further phylogenetic and structure-function studies of these RNA species.     

The tmRNA database (tmRDB).

This first release of the tmRNA database (tmRDB) contains 19 tmRNA sequences, a tmRNA sequence alignment with emphasis of base pairs that are supported by comparative sequence analysis, and a tabulation of tmRNA-encoded tag peptides. The tmRNADB also offers an RNA secondary structure diagram of the Escherichia coli tmRNA, as well as PDB-formatted coordinates for three-dimensional modeling. The data are available on the World Wide Web at http://www.uthct. edu/tmRDB/tmRDB.html     

The EMBL nucleotide sequence database

The EMBL Nucleotide Sequence Database (http://www.ebi.ac.uk/embl/) is maintained at the European Bioinformatics Institute (EBI) in an international collaboration with the DNA Data Bank of Japan (DDBJ) and GenBank at the NCBI (USA). Data is exchanged amongst the collaborating databases on a daily basis. The major contributors to the EMBL database are individual authors and genome project groups. Webin is the preferred web-based submission system for individual submitters, whilst automatic procedures allow incorporation of sequence data from large-scale genome sequencing centres and from the European Patent Office (EPO). Database releases are produced quarterly. Network services allow free access to the most up-to-date data collection via ftp, email and World Wide Web interfaces. EBI's Sequence Retrieval System (SRS), a network browser for databanks in molecular biology, integrates and links the main nucleotide and protein databases plus many specialized databases. For sequence similarity searching a variety of tools (e.g. Blitz, Fasta, BLAST) are available which allow external users to compare their own sequences against the latest data in the EMBL Nucleotide Sequence Database and SWISS-PROT.     

Small RNA database.

The small RNA database is a compilation of all the small size RNA sequences available to date from prokaryotic and eukaryotic organisms. About 500 small RNA sequences are in our database currently. The sources of individual RNAs and their GenBank accession numbers are also included. The small RNA database can be accessed through the World Wide Web(WWW). Our WWW URL is http://mbcr.bcm.tmc.edu/smallRNA/smallrna. html. The new small RNA sequences published since our last compilation are listed in this paper.     

The human (PEDB) and mouse (mPEDB) Prostate Expression Databases

The Prostate Expression Databases (PEDB and mPEDB) are online resources designed to allow researchers to access and analyze gene expression information derived from the human and murine prostate, respectively. Human PEDB archives more than 84 000 Expressed Sequence Tags (ESTs) from 38 prostate cDNA libraries in a curated relational database that provides detailed library information including tissue source, library construction methods, sequence diversity and sequence abundance. The differential expression of each EST species can be viewed across all libraries using a Virtual Expression Analysis Tool (VEAT), a graphical user interface written in Java for intra- and inter-library sequence comparisons. Recent enhancements to PEDB include (i) the development of a murine prostate expression database, mPEDB, that complements the human gene expression information in PEDB, (ii) the assembly of a non-redundant sequence set or ‘prostate unigene’ that represents the diversity of gene expression in the prostate, and (iii) an expanded search tool that supports both text-based and BLAST queries. PEDB and mPEDB are accessible via the World Wide Web at http://www.pedb.org and http://www.mpedb.org.