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THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 29,2022. Whole genome resource for the detection of transcription factor binding site clusters associated with conventional and microRNA encoding genes conserved between mouse and human gene orthologs

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• SciCrunch
• 17 years ago - by Anonymous

THIS RESOURCE IS NO LONGER IN SERVICE, documented April 24, 2017. The Genome Reviews database provides an up-to-date, standardized and comprehensively annotated view of the genomic sequence of organisms with completely deciphered genomes. Currently, Genome Reviews contains the genomes of archaea, bacteria, bacteriophages and selected eukaryota. Genome Reviews is available as a MySQL relational database, or a flat file format derived from that in the EMBL Nucleotide Sequence Database. An Ensembl-style browser is now available for Genome Reviews, providing a zoomable graphical view of all chromosomes and plasmids represented in the database. The location and structure of all genes is shown and the distribution of features throughout the sequence is displayed.

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• SciCrunch
• 17 years ago - by Anonymous

THIS RESOURCE IS NO LONGER IN SERVICE, documented on March 28, 2013. GIB is a comprehensive data repository of complete microbial genomes in the public domain. GIB will diffuse the genome sequence data and annotation in a day whenever the data is submitted to the International Nucleotide Sequence Databases (DDBJ, EMBL database and GenBank). You can explore any microbial genome by clone name, ORF name/number, function, gene name, product name, location, sequence (namely, homology search), and other features/qualifiers defined by INSD. The result of query is displayed either in graphics or in a table format.

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• SciCrunch
• 17 years ago - by Anonymous

GenoList is a resource for microbial genomes. It provides links to databases that give information on specific microbes. A link to the Genolist itself also incorporates many microbial genomes and search and analysis tools. Of the links provided on the GenoList homepage, species included are: Bacillus subtilis Escherichia coli Mycobacterium tuberculosis Mycobacterium leprae Mycobacterium bovis Mycobacterium ulcerans Listeria monocytogenes Legionella pneumophila Helicobacter pylori Mycoplasma pulmonis Synechocystis Anabaena Staphylococcus aureus Streptococcus pneumoniae Streptococcus agalactiae Photorhabdus luminescens Candida albicans Bacillus subtilis Escherichia coli Mycobacterium tuberculosis Mycobacterium leprae Mycobacterium bovis Mycobacterium ulcerans Listeria monocytogenes Legionella pneumophila Helicobacter pylori Mycoplasma pulmonis Synechocystis Anabaena Staphylococcus aureus Streptococcus pneumoniae Streptococcus agalactiae Photorhabdus luminescens Candida albicans

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• SciCrunch
• 17 years ago - by Anonymous

A database of high-throughput data being collected to understand comprehensively the living E. coli K-12 model cell. GenoBase is a public repository for sequence information, proteome, transcription, and metabolome data. The GenoBase contains columns labeled Gene, Synonym, ECK, Genome, ID, Left, Right, Direction, Description, Comment, and Status. The table displays two rows for each gene: one row shows data for the E. coli K-12 MG1655 genome; the other shows data for the E. coli K-12 W3110 genome. Left, Right, and direction give the coordinates and orientation of the gene. Search/Clip allows the user to find information in GenoBase based on gene, position, or DNA sequence. References is currently not fully operational. Other search allows execution of an SQL query., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

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• SciCrunch
• 17 years ago - by Anonymous

Genetics Home Reference provides consumer-friendly information about the effects of genetic variations on human health. Genetics Home Reference contains condition summaries (describing major features of genetic conditions), gene summaries (describing normal function, chromosomal location, etc), and gene family summaries.

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• SciCrunch
• 17 years ago - by Anonymous

A digital atlas of gene expression patterns in the mouse. Expression patterns are determined by non-radioactive in situ hybridization on serial tissue sections. An accompanying atlas based on maps of sagittal sections at embryonic day 14.5. E14.5 NMRI embryo was prepared, sectioned and imaged identically to the embryos used for in situ hybridization. Maps are accessed from the set viewer page using the appropriate button above the image directory. Both, the in situ hybridization section and the appropriate atlas section can be viewed side-by-side. Section thickness is 20 m and inter-section distance is 100 m. Tissue was stained with cresyl violet (Nissl-method). All sections were digitally scanned using a 5x objective. Structures annotated for gene expression are indicated in the maps with red pointers. Boundaries between brain regions are indicated with dashed yellow lines.

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• SciCrunch
• 17 years ago - by Anonymous

THIS RESOURCE IS NO LONGER IN SERVICE, documented June 14, 2013. GeneNote is a database of human genes and their expression profiles in healthy tissues. It is based on Weizmann Institute of Science DNA array experiments, which were performed on the Affymetrix HG-U95 set A-E. It offers: An expression profile (tissue vector) for each gene in the human genome Gene and tissue clustering based on expression profiles A full genome ranking procedure according to the gene''s tendency for tissue specificity, from tissue-specific to housekeeping genes.

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• SciCrunch
• 17 years ago - by Anonymous

Integrated system GeneNetWorks is designed for accumulation of experimental data, data navigation, data analysis, and analysis of dependencies in the field of gene expression regulation. It integrates the databases and programs for processing the data about structure and function of DNA, RNA, and proteins, together with the other information resources important for gene expression description. The unique property of above described system is that all the resources within the system GeneNetWorks are divided according to the natural hierarchy of molecular genetic systems and has the following levels: (1) DNA; (2) RNA; (3) proteins; and (4) gene networks. Each module contains: 1) experimental data represented as a database or some sample; 2) program for data analysis; 3) results of an automated data processing; 4) tools for the graphical representation of these data and the results of the data analyses.

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• SciCrunch
• 17 years ago - by Anonymous

GeneNest is a comprehensive visualization of gene indices of several organisms. The aim of GeneNest is to represent each gene by a single cluster of ESTs and/or mRNAs. Further subdivision of a cluster into contigs may be caused by alternative splicing, genomic sequences, or artifacts like chimeric sequences. Consensus sequence derived from GeneNest contigs are a basis for mapping genes onto the genome, and for analysis of splice isoforms. Organisms included are human, mouse, arabidopsis, zebrafish, drosophila, and sheep. human, mouse, arabidopsis, zebrafish, drosophila, sheep, EST, mRNA, alternative splicing, genomic sequences

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• SciCrunch
• 17 years ago - by Anonymous

GeneLoc presents an integrated map for each human chromosome, based on data integrated by the GeneLoc algorithm. GeneLoc includes further links to GeneCards, NCBI's Human Genome Sequencing, UniGene, and mapping resources. The GeneLoc algorithm creates an integrated map of the human genome. GeneLoc unifies gene collections, eliminates redundancies, and assigns each gene a meaningful location-based identifier, which also serves as its GeneCards ID. GeneLoc currently uses gene sets from NCBI and Ensembl. It compares these collections, deciding which entries should be consolidated and which are discrete. Since the gene annotations use the same assembly and coordinate scheme, GeneLoc effects this gene integration by comparing genomic locations. The resulting GeneLoc 'gene territory' reflects the range of the unified genes, taking into account every exon. Additionally, DNA segments, classified by categories (such as STSs mapped by various methods and EST clusters) are presented, alongside the genes, on a Megabase-scale map, with further information and links to relevant databases. Coming soon: genomic clones and more EST clusters will be added to the GeneLoc map. GeneLoc includes data from numerous resources, including the Genome Database, Whitehead Institute/MIT Center for Genome Research, Genethon, NCBI and others.

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• SciCrunch
• 17 years ago - by Anonymous

THIS RESOURCE IS NO LONGER IN SERVICE, documented on July 17, 2013. GeneTrees provides an interface to databases and analysis methods designed to explore the global phylogenetic patterns of gene homology groups within and across species. GeneTrees consists of several databases of pre-compiled alignments and gene phylogenies for a variety of taxonomic groups. Within each taxonomic group, genome-scale sequences have been globally searched for mutually consistent conserved homology groups.

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• SciCrunch
• 17 years ago - by Anonymous

GeneFarm is a database of structural and functional annotation of plant gene and protein families. The goal of the GeneFarm project is to obtain homogeneous, reliable, documented and traceable annotations for plant nuclear genes and gene products and to enter them into added-value database. The improved annotation will allow better data mining of the plant genomes (mainly Arabidopsis thaliana), and more secure planning and design of experiments. It is also a necessary step for building knowledge management tools for integrating plant genomic data, either for plant breeding or to get a broader interactive view of plant biological processes, like gene interaction networks. This re-annotation project, launched is mainly focused on gene families. A complete annotation pipeline using the most efficient prediction tools has been defined. The involved partners, each contributing with genes from his/her field of expertise, have exhaustively annotated families of homologous genes. A database named GeneFarm (Gene Families for Arabidopsis Management) gathers all these expert-curated annotations of plant gene families. Furthermore, collaboration with the Swiss Institute of Bioinformatics is underway to integrate the GeneFarm data into the protein knowledgebase Swiss-Prot.

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• SciCrunch
• 17 years ago - by Anonymous

GeneAnnot provides a revised and improved annotation of Affymetrix probe-sets from HG-U95, HG-U133 and HG-U133 Plus2.0. Probe-sets are related to GeneCards genes, by direct sequence comparison of probes to GenBank, RefSeq and Ensembl mRNA sequences, while assigning sensitivity and specificity scores to each probe-set to gene match. Where such matches are not found, probe-sets are annotated by their relation to GenBank mRNA sequences and UniGene clusters. The results are integrated with the GeneCards, GeneLoc and GeneNote databases. HG-U95, HG-U133, HG-U133

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• SciCrunch
• 17 years ago - by Anonymous

A large database of CATH protein domain assignments for ENSEMBL genomes and Uniprot sequences. Gene3D is a resource of form studying proteins and the component domains. Gene3D takes CATH domains from Protein Databank (PDB) structures and assigns them to the millions of protein sequences with no PDB structures using Hidden Markov models. Assigning a CATH superfamily to a region of a protein sequence gives information on the gross 3D structure of that region of the protein. CATH superfamilies have a limited set of functions and so the domain assignment provides some functional insights. Furthermore most proteins have several different domains in a specific order, so looking for proteins with a similar domain organization provides further functional insights. Strict confidence cut-offs are used to ensure the reliability of the domain assignments. Gene3D imports functional information from sources such as UNIPROT, and KEGG. They also import experimental datasets on request to help researchers integrate there data with the corpus of the literature. The website allows users to view descriptions for both single proteins and genes and large protein sets, such as superfamilies or genomes. Subsets can then be selected for detailed investigation or associated functions and interactions can be used to expand explorations to new proteins. The Gene3D web services provide programmatic access to the CATH-Gene3D annotation resources and in-house software tools. These services include Gene3DScan for identifying structural domains within protein sequences, access to pre-calculated annotations for the major sequence databases, and linked functional annotation from UniProt, GO and KEGG., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

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• SciCrunch
• 17 years ago - by Anonymous

A database of gene expression in tooth. It includes expression information on the initiation, bud, cap, bell, differentiation, and secretory stages, as well as on root development. The website also examines epithelial layers, growth factors and receptors, signaling molecules and transcription factors.

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• SciCrunch
• 17 years ago - by Anonymous

Genomic Distribution of structural Superfamilies identifies and classifies evolutionary related proteins at the superfamily level in whole genome databases. GenDiS has been curated in direct correspondence with SCOP and represents 4001 highly resolved domains in 1194 structural superfamilies across protein sequence databases. Sequences showing reliable homology to entries in SCOP and PASS2 databases have been obtained from the non-redundant protein sequence database and aligned. Similar alignments of the superfamily members are provided in the genome level. GenDiS provides a platform for cross genome comparison at the superfamily level. GenDis relates proteins sequence information across all strata of taxonomy. One may navigate through the database to obtain structural homologues across different levels in taxonomic classification. The nomenclature of the various genomes and their hierarchy is in direct correspondence with the taxonomy database maintained at the NCBI. Sequence homologues for the various structural members are obtained from the non-redundant protein sequence database employing sensitive sequence search methods. Multiple approaches such as PSI-BLAST, HMMsearch of the HMMer suite and an interacting motif constrained PHI-BLAST have been employed to identify homologues in the sequence databases.

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• SciCrunch
• 17 years ago - by Anonymous

GENATLAS contains relevant information with respect to gene mapping and genetic diseases. GENATLAS compiles the information relevant to the mapping efforts of the Human Genome Project. This information is collected from more than 48,000 articles in the literature, collected in more than 870 reviews. The articles are daily analyzed by annotators to update the GENATLAS database. Only the objects with a known cytogenetic location are retained. GENATLAS repertories three kinds of objects Genes database ( more than 21.000 entries) Phenotypes database ( 4104 entries , 2000 cloned) References database linked to the two previous ( more than 48000 entries)

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• SciCrunch
• 17 years ago - by Anonymous

GELBANK is a government project that provides an interactive interface for the comparison of 2DE patterns in the context of proteome sequence queries. Only proteomes of species with completed genomes (bacterial genomes, some eukaryotic genomes, human proteome) are presented in the database. The image database also contains not only scanned images, but also modeled gel patterns representing a collection of images (e.g. a master pattern for a sample). 2DE gel patterns are grouped by: tissue type, sample type, staining method used, separation technique used in the first dimension (by charge), the pH-range of the media used in first dimension, technique used in the second dimension (by size). Tools pertinent to the querying of two-dimensional gel-electrophoresis are implemented and integrated into database. When searching for sequences, tools that allow allow the discovery of sequences and alignment of multiple sequences are presented. Individual 2DE gel-patterns can be displayed or a collection of patterns can be animated.

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• SciCrunch
• 17 years ago - by Anonymous

THIS RESOURCE IS NO LONGER IN SERVCE, documented September 6, 2016. As a part of the FUNPEP project, we made a small collection of peptides, which are known to form these amyloid plaques (Known amyloidogenic peptides). Sequences, including respective animal analogues, were extracted from SWISSPROT, and aligned. These sequences and some words about the peptides can be found under the links in the table below. Some molecular modelling was also perfomed, to show some possible structures of amyloids. The peptides on these pages were not chosen because of some kind of sequence similarity, what is more, they hardly have any. Their common, and very starnge property is the ability to form amyloid plaques (or fibrils). The exact structure and the formation of these supermolacular structures are still subject of research, but there are lots of promising results.

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• SciCrunch
• 17 years ago - by Anonymous