The MEROPS database (http://www.merops.ac.uk) has been redesigned to accommodate increased amounts of information still in pages of moderate size that load rapidly. The information on each PepCard, FamCard or ClanCard has been divided between several sub-pages that can be reached by use of navigation buttons in a frame at the top of the screen. Several important additions have also been made to the database. Amongst these are CGI searches that allow the user to find a peptidase by name, its MEROPS identifier or its human or mouse chromosome location. The user may also list all published tertiary structures for a peptidase clan or family, and search for peptidase specificity data by entering either a peptidase name, substrate or bond cleaved. The PepCards, FamCards and ClanCards now have literature pages listing about 10 000 key papers in total, mostly with links to MEDLINE. Many PepCards now include a protein sequence alignment and data table for matching human, mouse or rat expressed sequence tags. FamCards and ClanCards contain Structure pages showing diagrammatic representations of known secondary structures of member peptidases or family type examples, respectively. Many novel peptidases have been added to the database after being discovered in complete genomes, libraries of expressed sequence tags or data from high-throughput genomic sequencing, and we describe the methods by which these were found.
The TBestDB database contains ∼370 000 clustered expressed sequence tag (EST) sequences from 49 organisms, covering a taxonomically broad range of poorly studied, mainly unicellular eukaryotes, and includes experimental information, consensus sequences, gene annotations and metabolic pathway predictions. Most of these ESTs have been generated by the Protist EST Program, a collaboration among six Canadian research groups. EST sequences are read from trace files up to a minimum quality cut-off, vector and linker sequence is masked, and the ESTs are clustered using phrap. The resulting consensus sequences are automatically annotated by using the AutoFACT program. The datasets are automatically checked for clustering errors due to chimerism and potential cross-contamination between organisms, and suspect data are flagged in or removed from the database. Access to data deposited in TBestDB by individual users can be restricted to those users for a limited period. With this first report on TBestDB, we open the database to the research community for free processing, annotation, interspecies comparisons and GenBank submission of EST data generated in individual laboratories. For instructions on submission to TBestDB, contact tbestdb@bch.umontreal.ca. The database can be queried at .
The organelle genome database GOBASE, now in its 21st release (June 2008), contains all published mitochondrion-encoded sequences (∼913 000) and chloroplast-encoded sequences (∼250 000) from a wide range of eukaryotic taxa. For all sequences, information on related genes, exons, introns, gene products and taxonomy is available, as well as selected genome maps and RNA secondary structures. Recent major enhancements to database functionality include: (i) addition of an interface for RNA editing data, with substitutions, insertions and deletions displayed using multiple alignments; (ii) addition of medically relevant information, such as haplotypes, SNPs and associated disease states, to human mitochondrial sequence data; (iii) addition of fully reannotated genome sequences for Escherichia coli and Nostoc sp., for reference and comparison; and (iv) a number of interface enhancements, such as the availability of both genomic and gene-coding sequence downloads, and a more sophisticated literature reference search functionality with links to PubMed where available. Future projects include the transfer of GOBASE features to NCBI/GenBank, allowing long-term preservation of accumulated expert information. The GOBASE database can be found at http://gobase.bcm.umontreal.ca/. Queries about custom and large-scale data retrievals should be addressed to gobase@bch.umontreal.ca.
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