Small RNA database.

The small RNA database is a compilation of all the small size RNA sequences available to date, including nuclear, nucleolar, cytoplasmic and mitochondria small RNAs from eukaryotic organisms and small RNAs from prokaryotic cells as well as viruses. Currently, approximately 600 small RNA sequences are in our database. It also gives the sources of individual RNAs and their GenBank accession numbers. The small RNA database can be accessed through the WWW (World Wide Web). Our WWW URL address is: http://mbcr.bcm.tmc. edu/smallRNA/smallrna.html . The new small RNA sequences published since our last compilation are listed in this paper (Table 1).     

Small RNA database.

The small RNA database is a compilation of all the small size RNA sequences available to date, including nuclear, nucleolar, cytoplasmic and mitochondrial small RNAs from eukaryotic organisms and small RNAs from prokaryotic cells as well as viruses. Currently, about 600 small RNA sequences are in our database. It also gives the sources of individual RNAs and their GenBank accession numbers. The small RNA database can be accessed through WWW(World Wide Web). Our WWW URL address 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 guide RNA database (3.0).

The RNA editing process within the mitochondria of kinetoplastid organisms is controlled by small, trans -acting RNA molecules referred to as guide RNAs. The guide RNA database is a compilation of published guide RNA sequences, currently containing 254 entries from 11 different organisms. Additional information includes RNA secondary and tertiary structure models, information on the gene localisation, literature citations and other relevant facts. The database can be accessed through the World Wide Web (WWW) at http://www.biochem.mpg.de/ goeringe/     

The guide RNA database.

Guide RNAs (gRNAs) are small, metabolically stable RNA molecules which perform a pivotal, template-like function during the RNA editing process in kinetoplastid protozoa. The gRNA database currently contains 250 guide RNA sequences as well as secondary and tertiary structure models and other relevant information. The database is made available as a hypertext document accessible via the World Wide Web (WWW) at the URL: http://www.biochem.mpg.de/ goeringe/     

The European Large Subunit Ribosomal RNA Database

The European Large Subunit Ribosomal RNA Database compiles all complete or nearly complete large subunit ribosomal RNA sequences available from public sequence databases. These are provided in aligned format and the secondary structure, as derived by comparative sequence analysis, is included. Additional information about the sequences such as literature references and taxonomic information is also included. The database is available from our WWW server at http://rrna.uia.ac.be/lsu/.     

The European large subunit ribosomal RNA database

The European Large Subunit (LSU) Ribosomal RNA (rRNA) database is accessible via the rRNA WWW Server at URL http://rrna.uia.ac.be/lsu/. It is a curated database that compiles complete or nearly complete LSU rRNA sequences in aligned form, and also incorporates secondary structure information for each sequence. Taxonomic information, literature references and other information about the sequences are also available, and can be searched via the WWW interface.     

Database on the structure of small ribosomal subunit RNA.

The Antwerp database on small ribosomal subunit RNA offers over 4300 nucleotide sequences (August 1995). All these sequences are stored in the form of an alignment based on the adopted secondary structure model, which in turn is corroborated by the observation of compensating substitutions in the alignment. Besides the primary and secondary structure information, literature references, accession numbers and detailed taxonomic information are also compiled. The complete database is made available to the scientific community through anonymous ftp and World Wide Web(WWW).     

HvrBase: compilation of mtDNA control region sequences from primates.

HvrBase is a compilation of human and ape mtDNA control region sequences. Sequences and related information on individuals, such as from where the sequences were obtained, is stored in three ASCII files as described previously. Moreover, the collection is also available as Mac/PC database application with a graphical user interface. It can be accessed through the WWW at URL http://www.eva.mpg.de/hvrbase. The current collection comprises 5846 human sequences from hypervariable region I (HVRI) and 2302 human sequences from hypervariable region II (HVRII). From apes, 295 HVRI sequences and 13 HVRII sequences are available.     

SELEX_DB: an activated database on selected randomized DNA/RNA sequences addressed to genomic sequence annotation

SELEX_DB is a novel curated database on selected randomized DNA/RNA sequences designed for accumulation of experimental data on functional site sequences obtained by using SELEX and SELEX-like technologies from the pools of random sequences. This database also contains the programs for DNA/RNA functional site recognition within arbitrary nucleotide sequences. The first release of SELEX_DB has been installed under SRS and is available through the WWW at http://wwwmgs.bionet.nsc.ru/mgs/systems/selex/     

The European small subunit ribosomal RNA database

The European database of the Small Subunit (SSU) Ribosomal RNA is a curated database that strives to collect all information about the primary and secondary structure of completely or nearly-completely sequenced rRNAs. Furthermore, the database compiles additional information such as literature references and taxonomic status of the organism the sequence was derived from. The database can be consulted via the WWW at URL http://rrna.uia.ac.be/ssu/. Through the WWW, sequences can be easily selected either one by one, by taxonomic group, or by a combination of both, and can be retrieved in different sequence and alignment formats.     

Database on the structure of large subunit ribosomal RNA.

The Antwerp database on large subunit ribosomal RNA now contains 607 complete or nearly complete aligned sequences. The alignment incorporates secondary structure information for each sequence. Other information about the sequences, such as literature references, accession numbers and taxonomic information is also available. Information from the database can be downloaded or searched on the rRNA WWW Server at URL http://rrna.uia.ac.be/     

PLMItRNA, a database for higher plant mitochondrial tRNAs and tRNA genes.

The PLMItRNA database contains information and multialignments of tRNA genes and molecules detected in higher plant mitochondria. It has been developed from a previous compilation of higher plant mitochondrial tRNA genes [Sagliano,A., Volpicella,M., Gallerani,R. and Ceci,L.R. (1998) Nucleic Acids Res., 26, 154-155] and implemented with data and sequences of tRNA molecules retrieved from the literature. The current version of the database reports information on 171 genes and 16 tRNA molecules from 24 plants. PLMItRNA is accessible via WWW at http://bio-www.ba.cnr.it:8000/srs/     

Database on the structure of large ribosomal subunit RNA.

The latest release of the large ribosomal subunit RNA database contains 429 sequences. All these sequences are aligned, and incorporate secondary structure information. The rRNA WWW Server at URL http://rrna.uia.ac.be/ provides researchers with an easily accessible resource to obtain the data in this database in a number of computer-readable formats. A new query interface has been added to the server. If necessary, the data can also be obtained by anonymous ftp from the same site.     

Compilation of DNA sequences of Escherichia coli K12 (ECD and ECDC; update 1995).

We have compiled the DNA sequence data for Escherichia coli available from the GenBank and EMBL data libraries and independently from the literature. Unlike the previous updates of our E.coli databases, we provide the most recent version preferentially via the World Wide Web System (use URL: http://susi.bio.unigiessen.de/usr/local/www++ +/html/ecdc.html). Our database includes an assembled set of contiguous sequences. Each of these contigs compiles all available sequence information, including those derived from a variety of elder sequences. The organization of the database allows one to find the exact physical location of each individual gene or regulatory region, even regarding discrepancies in nomenclature. The WWW program allows access into the original EMBL and SWISSPROT datafiles. A FASTA and BLAST search may be performed online. Besides the WWW format a flat file version may be obtained via ftp. The complete compilation, including a full set of genetic map data and the E.coli protein index, can be obtained in machine readable form from the EMBL data library as a part of the CD-ROM issue of the EMBL sequence database, released and updated every three months. After deletion of all detected overlaps a total of 3 333 878 individual bp was determined by the end of September 1995. This corresponds to a total of 71.71% of the entire E.coli chromosome consisting of about 4720 kbp. About 94 kbp (2%) are available additionally, but have not yet been definitely mapped.     

Database on the structure of large ribosomal subunit RNA.

The rRNA WWW Server at URL http://rrna.uia.ac.be/ now provides a database of 496 large subunit ribosomal RNA sequences. All these sequences are aligned, incorporate secondary structure information, and can be obtained in a number of formats. Other information about the sequences, such as literature references, accession numbers and taxonomic information is also available and searchable. If necessary, the data on the server can also be obtained by anonymous ftp.     

A new version of the RDP (Ribosomal Database Project).

The Ribosomal Database Project (RDP-II), previously described by Maidak et al. [ Nucleic Acids Res. (1997), 25, 109-111], is now hosted by the Center for Microbial Ecology at Michigan State University. RDP-II is a curated database that offers ribosomal RNA (rRNA) nucleotide sequence data in aligned and unaligned forms, analysis services, and associated computer programs. During the past two years, data alignments have been updated and now include >9700 small subunit rRNA sequences. The recent development of an ObjectStore database will provide more rapid updating of data, better data accuracy and increased user access. RDP-II includes phylogenetically ordered alignments of rRNA sequences, derived phylogenetic trees, rRNA secondary structure diagrams, and various software programs for handling, analyzing and displaying alignments and trees. The data are available via anonymous ftp (ftp.cme.msu. edu) and WWW (http://www.cme.msu.edu/RDP). The WWW server provides ribosomal probe checking, approximate phylogenetic placement of user-submitted sequences, screening for possible chimeric rRNA sequences, automated alignment, and a suggested placement of an unknown sequence on an existing phylogenetic tree. Additional utilities also exist at RDP-II, including distance matrix, T-RFLP, and a Java-based viewer of the phylogenetic trees that can be used to create subtrees.     

Aminoacyl-tRNA synthetases database Y2K

The aminoacyl-tRNA synthetases (AARS) are a diverse group of enzymes that ensure the fidelity of transfer of genetic information from DNA into protein. They catalyse the attachment of amino acids to transfer RNAs and thereby establish the rules of the genetic code by virtue of matching the nucleotide triplet of the anticodon with its cognate amino acid. Currently, 818 AARS primary structures have been reported from archaebacteria, eubacteria, mitochondria, chloro-plasts and eukaryotic cells. The database is a compilation of the amino acid sequences of all AARSs, known to date, which are available as separate entries or alignments of related proteins via the WWW at http://rose.man.poznan.pl/aars/index.html     

The RDP (Ribosomal Database Project).

The Ribosomal Database Project (RDP) is a curated database that offers ribosome-related data, analysis services and associated computer programs. The offerings include phylogenetically ordered alignments of ribosomal RNA (rRNA) sequences, derived phylogenetic trees, rRNA secondary structure diagrams, and various software for handling, analyzing and displaying alignments and trees. The data are available via anonymous FTP (rdp.life.uiuc.edu), electronic mail (server@rdp.life.uiuc.edu), gopher (rdpgopher.life.uiuc.edu) and WWW (http://rdpwww.life.uiuc.edu/ ). The electronic mail and WWW servers provide ribosomal probe checking, approximate phylogenetic placement of user-submitted sequences, screening for possible chimeric rRNA sequences, automated alignment, and a suggested placement of an unknown sequence on an existing phylogenetic tree.     

IRESdb: the Internal Ribosome Entry Site database

Internal Ribosome Entry Sites (IRES) are cis-acting RNA sequences able to mediate internal entry of the 40S ribosomal subunit on some eukaryotic and viral messenger RNAs upstream of a translation initiation codon. These sequences are very diverse and are present in a growing list of mRNAs. Novel IRES sequences continue to be added to public databases every year and the list of unknown IRESes is certainly still very large. The IRES database is a comprehensive WWW resource for internal ribosome entry sites and presents currently available general information as well as detailed data for each IRES. It is a searchable, periodically updated collection of IRES RNA sequences. Sequences are presented in FASTA form and hotlinked to NCBI GenBank files. Several subsets of data are classified according to the viral taxon (for viral IRESes), to the gene product function (for cellular IRESes), to the possible cellular regulation or to the trans-acting factor that mediates IRES function. This database is accessible at http://ifr31w3.toulouse.inserm.fr/IRESdatabase/.     

The Ribosomal Database Project (RDP).

The Ribosomal Database Project (RDP) is a curated database that offers ribosome-related data, analysis services and associated computer programs. The offerings include phylogenetically ordered alignments of ribosomal RNA (rRNA) sequences, derived phylogenetic trees, rRNA secondary structure diagrams and various software for handling, analyzing and displaying alignments and trees. The data are available via anonymous ftp (rdp.life.uiuc.edu), electronic mail (server@rdp.life.uiuc.edu), gopher (rdpgopher.life.uiuc.edu) and World Wide Web (WWW)(http://rdpwww.life.uiuc.edu/). The electronic mail and WWW servers provide ribosomal probe checking, screening for possible chimeric rRNA sequences, automated alignment and approximate phylogenetic placement of user-submitted sequences on an existing phylogenetic tree.