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Hypertext on cell culture availability extracted from the Cell Line Data Base of the Interlab Project. HyperCLDB includes links to records of OMIM, the Online Mendelian Inheritance in Man Catalogue, and now also links to the PubMed, database of bibliographic biomedical references, which are drawn primarily from MEDLINE and PREMEDLINE.

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• SciCrunch
• 17 years ago - by Anonymous

A database that serves as a repository for both, sequences of published functional siRNA molecules targeting human genes and important technical details of the corresponding gene silencing experiments. It aims at supporting the setup and actual procedure of specific RNAi experiments in human cells.

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• SciCrunch
• 17 years ago - by Anonymous

THIS RESOURCE IS NO LONGER IN SERVICE, documented on July 17, 2013. It contains information about segmental duplications in the human genome. The criteria used to identify regions of segmental duplication are: Sequence identity of at least 90, Sequence length of at least 5 kb, Not be entirely composed of repetitive elements. Background Previous studies have suggested that recent segmental duplications, which are often involved in chromosome rearrangements underlying genomic disease, account for some 5 of the human genome. We have developed rapid computational heuristics based on BLAST analysis to detect segmental duplications, as well as regions containing potential sequence misassignments in the human genome assemblies. Results Our analysis of the June 2002 public human genome assembly revealed that 107.4 of 3,043.1 megabases (Mb) (3.53) of sequence contained segmental duplications, each with size equal or more than 5 kb and 90 identity. We have also detected that 38.9 Mb (1.28) of sequence within this assembly is likely to be involved in sequence misassignment errors. Furthermore, we have identified a significant subset (199,965 of 2,327,473 or 8.6) of single-nucleotide polymorphisms (SNPs) in the public databases that are not true SNPs but are potential paralogous sequence variants. Conclusion Using two distinct computational approaches, we have identified most of the sequences in the human genome that have undergone recent segmental duplications. Near-identical segmental duplications present a major challenge to the completion of the human genome sequence. Potential sequence misassignments detected in this study would require additional efforts to resolve. The segmental duplication data and summary statistics are available for download. Data for Human Genome (based on the May 2004 Human Genome Assembly (hg17)) Visualize duplication relationships in GBrowse (GBrowse) Duplicon Pair relationships (GFF) Genes within duplication regions (HTML) Genome duplication content (MS Excel) The segmental duplication data can be visualized in a genome browser in the GBrowse section. Selected human genome annotation tracks (except the segmental duplication track) have also been obtained from UCSC and loaded into the genome browser. Detailed information (e.g. overlapping genes, overlapping clones, detailed alignment) can be obtained by clicking on a duplication cluster in GBrowse. Both keyword search and BLAT search are available. Analyses based on previous human genome assemblies can be found in the Previous Analyses section. Acknowledgments We thank The Centre for Applied Genomics at the Hospital for Sick Children (HSC) as well as collaborators worldwide. Supported by Genome Canada the Howard Hughes Medical Institute International Scholar Program (to S.W.S.) and the HSC Foundation.

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• SciCrunch
• 17 years ago - by Anonymous

The Human BAC Ends Database is a database of sequences from the ends of bacterial artificial chromosome (BAC) clones. A whole genome sequencing approach has been described in a map-as-you-go strategy. The complete sequence of a seed BAC is searched against a BAC end database and the minimally overlapping clones in each direction are selected for sequencing. As coverage increases, BAC end sequences provide samples for whole genome survey. It currently contains 743,000 end sequences from 470,000 clones (20 X clone coverage and 12% sequence coverage), generated by TIGR, UofWashington and CalTech, providing a sequence marker every 5 kb across the genome. The coverage by paired-ends on chromosome 22 is over 5X. The project is funded by DOE.

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• SciCrunch
• 17 years ago - by Anonymous

The Human Gene Expression Index (HuGE Index) aims to provide a comprehensive database to further our understanding of the expression of human genes in normal human tissues. mRNA expression levels of thousands of genes are obtained using high-density oligonucleotide array technology and used to create a public database. The website also provides interactive tools for researchers to query and visualize data over the Internet. To facilitate data analysis, genes are alsocross-referenced with their annotation in the LocusLink database at NCBI.

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• SciCrunch
• 17 years ago - by Anonymous

HPMR is a database of human plasma membrane ligands and receptors. Users can search for ligands or receptors to reveal their pairing partners and browse through ligand or receptor families to identify ligand-receptor relationships. Users can also submit their own microarray data to perform online genome-wide online searches for paracrine/autocrine signaling systems. Survey of transcriptomes based on liganded receptome allows the discovery of paracrine/autocrine signaling for known ligand-receptor pairs in previously uncharacterized tissues or developmental stages.

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• SciCrunch
• 17 years ago - by Anonymous

Database that provides human protein interaction information and integrated interaction and also finds proteins from databases that can potentially react with proteins submitted by users. The human protein interaction information was pre-computed by a statistical method from existing structural and experimental data, while the integrated human protein interactions are derived from BIND, DIP and HPRD. A score composed of three parts is assigned to the predicted interaction data, and those interactions with high scores were found reliable. HPID allows the user to use the protein IDs in EMBL, Ensembl, MIM, RefSeq, HPRD and NCBI to search protein interactions of interest. A set of web-based software tools has also been developed so that users can visualize and analyze protein interaction networks.

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• SciCrunch
• 17 years ago - by Anonymous

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 11th,2023. The database HOX Pro contains information about organization, functions and evolution of gene ensembles, key roles in which play homeobox-genes. It is aimed at: 1. analysis and classification of regulatory and coding regions in diverse homeobox and related genes; 2. describing mutations and knock-outs of hox-genes, as well as hereditary diseases related to these genes; 3. graphical representation, comparisons and classification of hox-genes expression patterns and profiles (sea urchin blastula, Drosophila blastoderm and imaginal discs, vertebrate limbs, mammalian brain, human EC cells); 4. comparative analysis of organization of hox-based genetic networks the nematode Caenorhabditis elegans the sea urchins Strongylocentrotus purpuratus and other echinids, the fruit flies Drosophila melanogaster and D.virilis, the vertebrates chicken and mouse; 5. analysis of phylogeny and evolution of homeobox genes and clusters.

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• SciCrunch
• 17 years ago - by Anonymous

HumHot is a collection of human meiotic hot spots obtained from the literature along with interesting information on meiotic recombination and molecular features of meiotic hot spots. It is also updated as more hot spots get discovered in the human genome. The database can be queried by hot spot name or chromosome number.

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• SciCrunch
• 17 years ago - by Anonymous

THIS RESOURCE IS NO LONGER IN SERVICE, documented on July 15, 2013. A database system for retrieve human genome information in different data sources that are available to public. The information you could find here is automatically extracted from the genetic databases and shown with all data having the identifiers in common and linking to one another. HOWDY facilitates obtaining information of human genes by using official symbols and aliases approved by HGNC, GDB and Entrez Gene. It also provides a graphical view of the Human Genome maps for the finished contigs as well as radiation hybrid maps.

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• SciCrunch
• 17 years ago - by Anonymous

It provides information about the evolutionary history of the residues on the interface and represents which residues are highly conserved on the interface. In this way, functionally and structurally important residues on the interface can be distinguished. Hotsprint contains overall properties of the interface such as number of computational hot spots on the interface, number of conserved residues on the interface, average conservation score of interface residues and buried ASA of the interface. Additionally, residues of the interface along with their position, name, conservation score, ASA in monomer, ASA in complex, type (contacting interface residue, neighboring interface residue or none) and whether the residue is computational hot spot or not information are presented.

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• SciCrunch
• 17 years ago - by Anonymous

HORDE (The Human Olfactory Data Explorer) is a database of human Olfactory Receptors (ORs), the largest multigene family in multicellular organisms. You will find here information on the OR proteins, their gene structure and their genomic organization. Also available are OR repertoires of other mammalian species, along with a set of analysis tools. human olfactory receptor, :OR, OR proteins, olfactory receptor, THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

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• SciCrunch
• 17 years ago - by Anonymous

Hoppsigen is a nucleic database of homologous processed pseudogenes. It contains 5,823 human retroelements and 3,934 mouse retroelements. These retroelements were annotated and stored in the database HOPPSIGEN (Homologous processed pseudogenes). Sequences were grouped in families considering their homologies. The database contains 3,168 families of exclusively human (1,966) or mouse retroelements (1,202) and 323 families containing human and mouse retroelements. 5,206 human retroelements were annotated as processed pseudogenes (respectively 3,428 mouse retroelements). The database contains functional genes from ENSEMBL homologous to Hoppsigen retroelements.

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• SciCrunch
• 17 years ago - by Anonymous

THIS RESOURCE IS NO LONGER IN SERVICE, documented on June 23, 2013. Homophila utilizes the sequence information of human disease genes from the NCBI OMIM (Online Mendelian Inheritance in Man) database in order to determine if sequence homologs of these genes exist in the current Drosophila sequence database (FlyBase). Sequences are compared using NCBI's BLAST program. The database is updated weekly and can be searched by human disease, gene name, OMIM number, title, subtitle and/or allelic variant descriptions.

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• SciCrunch
• 17 years ago - by Anonymous

A database of homologous invertebrate genes, structured under ACNUC sequence database management system. It allows one to select sets of homologous genes among invertebrate species, and to visualize multiple alignments and phylogenetic trees. The database itself contains all invertebrate protein sequences from UniProt (SWISS-PROT+TrEMBL), with some data corrected, clarified or completed (notably to address the problem of redundancy and orthology/paralogy) and with some annotation modifications. It contains also all the corresponding nucleotide sequences in EMBL. Homologous proteins are classified into families and multiple alignments and phylogenetic trees are computed for each family. Sequences and related information have been structured in an ACNUC database. Thus, HOINVGEN is particularly useful for comparative sequence analysis, phylogeny and molecular evolution studies. More generally, HOINVGEN gives an overall view of what is known about a peculiar gene family.

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• SciCrunch
• 17 years ago - by Anonymous

THIS RESOURCE IS NO LONGER IN SERVICE, documented on July 16, 2013. It provides access to the results of tests for positive selection in 14,000 human genes. Multiple alignments of protein-coding regions of genes from human and other mammals were extracted from whole-genome alignments available from UC-Santa Cruz. Each gene was analyzed using the maximum likelihood tests of selection using PAML. Branch, site, and branch+site tests were performed, each with at least one matching null model.

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• SciCrunch
• 17 years ago - by Anonymous

THIS RESOURCE IS NO LONGER IN SERVICE, documented on July 16, 2013. A database of biochemical compound information. All files are available for download, and all entries are cataloged by accession number. Klotho is part of a larger attempt to model biological processes, beginning with biochemistry.

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• SciCrunch
• 17 years ago - by Anonymous

A human mitochondrial resource aimed at supporting population genetics and mitochondrial disease studies. It consists of a database of Human Mitochondrial Genomes annotated with population and variability data, the latter estimated through the application of a new approach based on site-specific nucleotidic and aminoacidic variability calculation (SiteVar and MitVarProt programs). The goals of HmtDB are: to collect and integrate the publicly available human mitochondrial genomes data; to produce and provide the scientific community with site-specific nucleotidic and aminoacidic variability data estimated on all the collected human mitochondrial genome sequences; to allow any researcher to analyse his own human mitochondrial sequences (both complete and partial mitochondrial genomes) in order to automatically detect the nucleotidic variants compared to the revised Cambridge Reference Sequence (rCRS) and to predict their haplogroup paternity. HmtDBs first release contains 1255 human mitochondrial genomes derived from public databases (GenBank and MitoKor). The genomes have been stored and analysed as a whole dataset and grouped in continent-specific subsets (AF: Africa, AM: America, AS: Asia, EU: Europe, OC: Oceania). :The multialignment and site-variability analysis tools included in HmtDB are clustered in two Work Flows: the Variability Generation Work Flow (VGWF) and the Classification Work Flow (CWF), which are applied both to human mitochondrial genomes stored in the database and to newly sequenced genomes submitted by the user, respectively., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

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• SciCrunch
• 17 years ago - by Anonymous

Curated collection of human metabolite and human metabolism data which contains records for endogenous metabolites, with each metabolite entry containing detailed chemical, physical, biochemical, concentration, and disease information. This is further supplemented with thousands of NMR and MS spectra collected on purified reference metabolites.

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• SciCrunch
• 14 years ago - by Anonymous

Histone Database is a database of histones and their corresponding sequences. Sequence- and text-based searches were performed on NCBI's redundant and non-redundant (nr) peptide sequence databases. These databases are derived from GenBank, EMBL, and DDBJ translated DNA coding regions, plus protein sequences from the PDB (Protein Data Bank), SWISS-PROT, the PIR (Protein Information Resource), and the PRF (Protein Research Foundation). :Users can search by keyword, sequence fragment, category, organism, and redundancy of the set.

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• SciCrunch
• 17 years ago - by Anonymous