The HUSAR Bioinformatics Lab at the German Cancer Research Center (DKFZ, Heidelberg) provides cutting-edge bioinformatics support and training to the scientist of the (post-) genomic era. This includes the Heidelberg Unix Sequence Analysis Resources (HUSAR), a large collection of essential sequence analysis tools. We provide the most up-to-date databases and software packages. Our main package - HUSAR - offers more than 260 applications for DNA and protein analysis. In addition to the latest, complete version of the GCG package (about 50% of our applications), you can use tools developed by us and by other ranking researchers in the bioinformatics field. We offer more than 200 databases, which are updated as soon as new versions become available. The major databases are updated every night (e.g. EMBL, GenBank) or weekly (Swissprot, Unigene). With HUSAR you can analyse the newest sequence data available. This is essential, as the DNA databases currently double their sizes in less than 9 months. ... [Information of the supplier]
We present a neural network based method (ChloroP) for identifying chloroplast transit peptides and their cleavage sites. Using cross-validation, 88% of the sequences in our homology reduced training set were correctly classified as transit peptides or nontransit peptides. This performance level is well above that of the so far only publicly available chloroplast localization predictor PSORT. Cleavage sites are predicted using a scoring matrix derived by an automatic motif-finding algorithm. Approximately 60% of the known cleavage sites in our sequence collection were predicted to within +- 2 residues from the cleavage sites given in SWISS-PROT. An analysis of 715 A. thaliana sequences from SWISS-PROT suggests that the ChloroP method should be useful for the identification of putative transit peptides in genome-wide sequence data. ... [Information of the supplier]
The Eukaryotic Promoter Database is an annotated non-redundant collection of eukaryotic POL II promoters, for which the transcription start site has been determined experimentally. Access to promoter sequences is provided by pointers to positions in nucleotide sequence entries. The annotation part of an entry includes description of the initiation site mapping data, cross-references to other databases, and bibliographic references. EPD is structured in a way that facilitates dynamic extraction of biologically meaningful promoter subsets for comparative sequence analysis. (...) A eukaryotic promoter is defined as a DNA sequence around a transcription initiation site. The position reference to the initiation site is therefore the central part of a promoter entry. ... [Information of the supplier]
Genomes Online Database is a World Wide Web resource for comprehensive access to information regarding complete and ongoing genome projects around the world. GOLD provides the largest available and most detailed monitoring of genome sequencing projects. [Information of the supplier]
GermOnline is a cross-species community annotation knowledgebase that provides microarray data relevant for the mitotic and meiotic cell cycle as well as gametogenesis. Importantly, GermOnline also integrates knowledge about genes important for sexual reproduction that is contributed and updated by members of the scientific community in collaboration with professional curators. ... [Information of the supplier]
Based on the mapping of the human genome and the development of information databases, a broad description of genes transcribed in blood cells is now known. Hembase was developed to provide worldwide access to those genetic-based studies performed by scientists in the Molecular Biology and Genetics Section, Molecular Medicine Branch, Division of Intramural Research, National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK). This project represents the shared goal of several individuals and groups (credits) interested in disseminating genomic information on the World Wide Web. ... [Information of the supplier]
Metazome is a database and graphical user interface enabling comparative genomic studies within the Metazoa. As of version 1.1, the database houses eleven sequenced animal genomes and is constantly growing as new genomes become available. Each gene has been annotated with PFAM, KOG, and PANTHER assignments, and publicly available annotations from RefSeq, SwissProt, Ensembl, and JGI are hyper-linked and searchable. For comparative studies, various clustering methods have been applied to construct orthologous groups of genes that represent the modern descendents of ancestral gene sets at key phylogenetic nodes, including the ancestral tetrapod and vertebrate. These clusterings allow easy access to clade specific orthology/paralogy relationships as well as clade specific genes and gene expansions. Position specific profiles will be made available shortly and gene phylogenetic trees are available now for each cluster to enable deeper comparative studies. ... [Information of the supplier]
The MicrobesOnline genome database contains over 300 prokaryotic genomes. All genomes are automatically analyzed through the VIMSS genome pipeline. We use publicly available sequence analysis tools and databases to search for homologs (NCBI BLAST, SwissProt, COG) and protein domains (InterPro), to assign gene ontologies (Gene Ontology Consortium) and EC numbers and to map the metabolic pathways (KEGG). We then link the orthology relationships between genes, predict operon structures and regulon networks. Most of the genomes are downloaded from NCBI and genes are parsed from GenBank files. When an incomplete genome is directly downloaded from a sequencing center, we predict protein coding genes using CRITICA and Glimmer, tRNA genes using tRNAscan and other RNA genes by BLASTn. All of the info in the VIMSS genome database is freely available on our website. ... [Information of the supplier]
The DNA amount in the unreplicated gametic nucleus of an organism is referred to as its C-value, irrespective of the ploidy level of the taxon. The Plant DNA C-values Database currently contains data for 3927 different Embryophyte plant species. It combines data from the Angiosperm DNA C-values Database (release 4.0, Jan. 2003), the Pteridophyte DNA C-values Database (release 2.0, Jan. 2003 ) together with the Gymnosperm DNA C-values Database (release 2.0, Jan. 2003) and the Bryophyte DNA C-values Database (release 1.1, Jan. 2003). ... [Information of the supplier]
The Consortium for the Barcode of Life (CBOL) is an international initiative devoted to developing DNA barcoding as a global standard in taxonomy. CBOL has more than 130 Member Organizations from 40 countries. DNA Barcoding is a technique that uses a short gene sequence from a standardized region of the genome as a diagnostic “biomarker” for species. Different species have different DNA barcodes, making it possible to use barcodes to: (1) identify specimens, (2) discover possible new species, and (3) to make taxonomy more effective for science and society. ... [Information of the supplier]