Ribosomal 5S RNA (5S rRNA) is an integral component of the large ribosomal subunit in all known organisms with the exception only of mitochondrial ribosomes of fungi and animals. It is thought to enhance protein synthesis by stabilization of a ribosome structure. This paper presents the updated database of 5S rRNA and their genes (5S rDNA). Its short characteristics are presented in the Introduction. The database contains 2280 primary structures of 5S rRNA and 5S rRNA genes. These include 536 eubacterial, 61 archaebacterial, 1611 eukaryotic and 72 organelle sequences. The database is available on line through the World Wide Web at http://biobases.ibch.poznan.pl/5SData/. (+info)
The tmRNA Website: invasion by an intron.
(50/2093)
tmRNA (also known as 10Sa RNA or SsrA) plays a central role in an unusual mode of translation, whereby a stalled ribosome switches from a problematic mRNA to a short reading frame within tmRNA during translation of a single polypeptide chain. Research on the mechanism, structure and biology of tmRNA is served by the tmRNA Website, a collection of sequences for tmRNA and the encoded proteolysis-inducing peptide tags, alignments, careful documentation and other information; the URL is http://www.indiana.edu/~tmrna. Four pseudoknots are usually present in each tmRNA, so the database is rich with information on pseudoknot variability. Since last year it has doubled (227 tmRNA sequences as of September 2001), a sequence alignment for the tmRNA cofactor SmpB has been included, and genomic data for Clostridium botulinum has revealed a group I (subgroup IA3) intron interrupting the tmRNA T-loop. (+info)
The European database on small subunit ribosomal RNA.
(51/2093)
The European database on SSU rRNA can be consulted via the World WideWeb at http://rrna.uia.ac.be/ssu/ and compiles all complete or nearly complete small subunit ribosomal RNA sequences. Sequences are provided in aligned format. The alignment takes into account the secondary structure information derived by comparative sequence analysis of thousands of sequences. Additional information such as literature references, taxonomy, secondary structure models and nucleotide variability maps, is also available. (+info)
PALS db: Putative Alternative Splicing database.
(52/2093)
PALS db is a collection of Putative Alternative Splicing information from 19 936 human UniGene clusters and 16 615 mouse UniGene clusters. Alternative splicing (AS) sites were predicted by using the longest messenger RNA (mRNA) sequence in each UniGene cluster as the reference sequence. This sequence was aligned with related sequences in UniGene and dbEST to reveal the AS. This information was presented with six features: (i) literature aliases were used to improve the result of a gene name search; (ii) the quality of a prediction can be easily judged from the color-coded similarity and the scaled length of an alignment; (iii) we have clustered those EST sequences that support the same AS site together to enhance the users' confidence on a prediction; (iv) the users can also set up the alignment criteria interactively to recover false negatives; (v) tissue distribution can be displayed by placing the mouse cursor over an alignment; (vi) gene features will be analyzed at foreign sites by submitting the selected mRNA or its encoded protein as a query. Using these features, the users cannot only discover putative AS sites in silico, but also make new observations by combining AS information with tissue distributions or with gene features. PALS db is available at http://palsdb.ym.edu.tw/. (+info)
ExInt: an Exon Intron Database.
(53/2093)
The Exon/Intron Database (ExInt) stores information of all GenBank eukaryotic entries containing an annotated intron sequence. Data are available through a retrieval system, as flat-files and as a MySQL dump file. In this report we discuss several implementations added to ExInt, which is accessible at http://intron.bic.nus.edu.sg/exint/newexint/exint.html. (+info)
SELEX_DB: a database on in vitro selected oligomers adapted for recognizing natural sites and for analyzing both SNPs and site-directed mutagenesis data.
(54/2093)
SELEX_DB is an online resource containing both the experimental data on in vitro selected DNA/RNA oligomers (aptamers) and the applets for recognition of these oligomers. Since in vitro experimental data are evidently system-dependent, the new release of the SELEX_DB has been supplemented by the database SYSTEM storing the experimental design. In addition, the recognition applet package, SELEX_TOOLS, applying in vitro selected data to annotation of the genome DNA, is accompanied by the cross-validation test database CROSS_TEST discriminating the sites (natural or other) related to in vitro selected sites out of random DNA. By cross-validation testing, we have unexpectedly observed that the recognition accuracy increases with the growth of homology between the training and test sets of protein binding sequences. For natural sites, the recognition accuracy was lower than that for the nearest protein homologs and higher than that for distant homologs and non-homologous proteins binding the common site. The current SELEX_DB release is available at http://wwwmgs.bionet.nsc.ru/mgs/systems/selex/. (+info)
VirOligo: a database of virus-specific oligonucleotides.
(55/2093)
VirOligo is a database of virus-specific oligonucleotides. The VirOligo database consists of two tables, Common data and Oligo data. The Oligo data table contains PCR primers and hybridization probes used for detection of viral nucleic acids and the Common data table contains the experimental conditions used in their detection. Each oligonucleotide entry contains links to PubMed, GenBank, NCBI Taxonomy databases and BLAST. As of July 2001, the VirOligo database contains a complete listing of oligonucleotides specific to viral agents associated with bovine respiratory disease that were published in English in peer-reviewed journals. The viruses are bovine herpes virus types 1, 3, 4 and 5, bovine viral diarrhea virus, bovine parainfluenza 3 virus, bovine respiratory syncytial virus, bovine adenovirus, bovine rhinovirus, bovine coronavirus, bovine reovirus, bovine enterovirus and alcelaphine herpesvirus-1. The VirOligo database is being expanded to other viruses and can be accessed through the Internet at http://viroligo.okstate.edu/. (+info)
HERVd: database of human endogenous retroviruses.
(56/2093)
The human endogenous retroviruses database (HERVd) is maintained at the Institute of Molecular Genetics, Academy of Sciences of the Czech Republic, and is accessible via the World Wide Web at http://herv.img.cas.cz. The HERVd provides complex information on and analysis of retroviral elements found in the human genome. It can be used for searches of individual HERV families, identification of HERV parts, graphical output of HERV structures, comparison of HERVs and identification of retrovirus integration sites. (+info)