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THIS RESOURCE IS NO LONGER IN SERVICE, documented August 19, 2016. A reference database on Nuclear Hormone Receptors. It is a bioinformatic database of nuclear receptors. NuReBase Version 4 is hosted on the PBIL server, contains protein and DNA sequences arranged according to the official nomenclature. In addition, for each group of homologous genes a phylogenetic tree and a protein alignment is provided. NuReBase also contains EMBL sequences and annotations for proteins and DNA, enriched with nuclear hormone receptor-specific information. The core of the NuReBase database is reviewed and this core is complemented by another database, NuReBase_DAILY, which is automatically updated every 24 hours. Recently, the NuReBase database has been expanded. It now includes data on alternative transcripts for each gene in the database and expression data for human and mouse nuclear receptors.

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• SciCrunch
• 17 years ago - by Anonymous

A database covering eight category functional interactions between noncoding RNAs (except tRNAs and rRNAs) and proteins related biomacromolecules (proteins, mRNAs and genomic DNAs) in six model organisms. Functional interactions imply both physical interactions between the ncRNA and protein, and other forms of interaction where the combination of an ncRNA and an mRNA or a genomic DNA sequence elicits a cellular reaction. This database is distinguished from other biomolecular interaction database by: 1. The data of NPInter is novel, in the sense that no earlier database has especially cataloged this type of data (ncRNA-protein interactions). The database now contains more than 700 published functional interactions from the six organisms E. coli, yeast, worm, fly, mouse and human in which functional interactions experiments have been concentrated. The amount of data is not large, but the NPInter covers almost all experimentally verified ncRNA functional interaction data which had been published before the end of last year. 2. The ncRNA functional interaction data are entered into NPInter only following publication in books or peer-reviewed journals. Entry is done manually by a curator, and thereafter double-checked by a second curator. 3. We introduce a classification of the functional interaction data, which is based on the functional interaction process the ncRNA takes part in. 4. NPInter also provides an efficient search option, allowing recovery of interactions, related publications and other information., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

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• SciCrunch
• 17 years ago - by Anonymous

A searchable database of information on proteins that are localised to the nucleus of vertebrate cells. The NPD contains information on >2000 vertebrate proteins (mainly those from mouse and human) that are thought to, or known to, be localised to the cell nucleus. Where known, the sub-nuclear compartment where the proteins have been found are reported. Also stored is information on the amino acid sequence, predicted protein size and isoelectric point, as well as any repeats, motifs or domains within the protein sequence. Biological and molecular functions of the proteins are described using GO terms. Where appropriate, links to other databases are provided (e.g. Entrez, SWISS-PROT, OMIM, PubMed, PubMed Central).

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• SciCrunch
• 17 years ago - by Anonymous

A platform that includes a database of nonribosomal peptides together with tools for their analysis. Norine currently contains more than 1000 peptides. The name Norine stands for Nonribosomal peptides, with "ine" as a typical ending of peptide names. For each peptide, the database stores its structure as well as various annotations such as the biological activity, producing organisms, bibliographical references and others. The database can be queried in order to search for peptides through their annotations as well as through their monomeric structure. In the latter case, the user can specify either the whole structure or a structural pattern (possibly including "undefined monomers") of the searched peptide.

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• SciCrunch
• 17 years ago - by Anonymous

Collection of non-coding RNAs (excluding tRNAs and rRNAs) as an integrated knowledge database. Used to get text information such as class,name,location,related publication,mechanism through which it exerts its function, view figures which show their location in the genome or in a specific DNA fragment, and the regulation elements flanking the ncRNA gene sequences.

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• SciCrunch
• 17 years ago - by Anonymous

The National Microbial Pathogen Data Resource provides curated annotations in an environment for comparative analysis of genomes and biological subsystems, with an emphasis on the food-borne pathogens Campylobacter, Listeria, Staphylococcus, Streptococcus, and Vibrio; as well as the STD pathogens Chlamydiaceae, Haemophilus, Mycoplasma, Neisseria, Treponema, and Ureaplasma. This edition of the NMPDR includes 47 archaeal, 725 bacterial, and 29 eukaryal genomes with 3,257,100 genetic features, of which 1,338,895 are in FIGfams curated using 616 active subsystems. ''''''Notice to NMPDR Users'''''' - The NMPDR BRC contract ended in December 2009. At that time we ceased maintenance of the NMPDR web resource and data. Bacterial data from NMPDR has been transferred to PATRIC (http://www.patricbrc.org), a new consolidated BRC for all NIAID category A-C priority pathogenic bacteria. NMPDR was a collaboration among researchers from the Computation Institute of the University of Chicago, the Fellowship for Interpretation of Genomes (FIG), Argonne National Laboratory, and the National Center for Supercomputing Applications (NCSA) at the University of Illinois.

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• SciCrunch
• 16 years ago - by Anonymous

NRESTdb is an online resource which provides access to sequence, clustering, classification and annotation data of ESTs from rubber. The NRESTdb consists of EST sequences, BLASTX search results against the non-redundant protein database (NR), Pfam and InterPro, annotations based on KOG, Inparanoid and GO classifications, enhanced datasets related to rubber research topics of interest and search tools to facilitate user navigation. The NRESTdb resources and facilities are aimed at providing a genomic data resource to facilitate rubber biotechnology research. The development of NRESTdb is a collaborative project of the Malaysia Genome Institute EST database working group and the Malaysian Rubber Board genomics group.

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• SciCrunch
• 16 years ago - by Anonymous

NMP-db is a database of nuclear matrix associated proteins. The NMP-db consists of two parts. The first part is the actual literature based NMP-db, containing all nuclear matrix proteins (NMPs) that were originally found in PubMed. The second part is a database of homologues to the NMP-db proteins. This database is called NMP-db(hom) and contains proteins which have at least an HSSP-value of 55 to one of the proteins in the NMP-db. The NMP-db holds informations about the protein names, their organism and the cell-type in which NM association was observed. Also links to the respective PubMed abstracts are given in each entry. Additionally, we provide information about predictions of secondary structure, solvent accessibility, coiled-coil regions and domain-architecture, as well as the sequence, links to PDB (database of 3D-structures), molecular weight, theoretical pI, links to SWISS-2DPAGE, OMIM, PEP and many other databases. If available, we also list regions in a protein sequence that are known to be cruicial for NM-targeting. Finally, links to the S/MARt DB allow users to find DNA-regions that bind to NMPdb proteins.

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• SciCrunch
• 17 years ago - by Anonymous

A method for predicting in vivo kinase-substrate relationships, that augments consensus motifs with context for kinases and phosphoproteins. This website allows a user to browse/search and investigate predictions made using the NetworKIN algorithm. The site is powered by the latest phosphoproteome in Phospho.ELM. Alternatively users can submit their own protein sequences and phosphorylation sites and obtain new NetworKIN predictions.

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• SciCrunch
• 17 years ago - by Anonymous

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 17,2023. Affymetrix is a partially commercial resource that provides DNA Analysis Arrays, Expression Analysis Arrays, Gene Regulation Analysis, and Microarrays. It also provides reagents and assays, instruments, software, and services for a fee. Information is provided for Rats, Humans, and Mice.Affymetrix is now Applied Biosystems, brand of DNA microarray products sold by Thermo Fisher Scientific that originated with an American biotechnology research and development and manufacturing company of the same name.

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• SciCrunch
• 17 years ago - by Anonymous

The home page of the parasitic nematode EST project at Washington University's Genome Sequencing Center, St. Louis. It was established in 2000 as a component of the NIH-NIAID grant "A Genomic Approach to Parasites from the Phylum Nematoda."

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• SciCrunch
• 17 years ago - by Anonymous

It is intended to provide information on the sequences and functions of transcripts which do not code for proteins, but perform regulatory roles in the cell. Currently, the database includes over 30,000 individual sequences from 99 species of Bacteria, Archaea and Eukaryota. The primary source of sequences included in the database was the GenBank. Additional annotation information for mouse and human ncRNAs was derived from FANTOM3 database and H-inviational Integrated Database of Annotated Human Genes version 3.4, respectively. Genome mapping information was derived from tha data available at the UCSC Genome Browser site. The sequences and annotations of small cytoplasmic RNAs from bacteria, for which annotation is lacking in the genome sequences, were derived from the Rfam database. The microRNAs or snoRNAs which were available in previous editions, as well as other housekeeping (infrastructural) RNAs (e.g. rRNA, tRNA, snRNA, SRP RNA) are not included in our database to avoid redundancy with more specialized databases which emerged in recent years.

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• SciCrunch
• 17 years ago - by Anonymous

A collection of programs for the removal of noise from 454 sequenced PCR amplicons. This project also includes the Perseus algorithm for chimera removal.

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• SciCrunch
• 13 years ago - by Anonymous

Narcisse is a comparative genome browser. The aim is to provide a simple and intuitive access to the results of comparison of genomes completely or partially sequenced. The principle of construction of conserved segments based on the idea that the concept of conservation depends on the level of resolution. The number of levels of conservation is fixed, more or less arbitrary for animals 5 and 2 for the other kingdoms. Narcisse software allows users to move between these levels of conservation.

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• SciCrunch
• 17 years ago - by Anonymous

A database of multiple position specific scoring matrices of protein domain families with constant alignments. Representation of multiple sequence alignments of protein families in terms of position-specific scoring matrices (PSSMs) is commonly used in the detection of remote homologues. A PSSM is generated with respect to one of the sequences involved in the multiple sequence alignment as a reference. We have shown recently that the use of multiple PSSMs corresponding to an alignment, with several sequences in the family used as reference, improves the sensitivity of the remote homology detection dramatically. MulPSSM contains PSSMs for a large number of sequence and structural families of protein domains with multiple PSSMs for every family. The approach involves use of a clustering algorithm to identify most distinct sequences corresponding to a family. With each one of the distinct sequences as reference, multiple PSSMs have been generated. The current release of MulPSSM contains ~33 000 and ~38 000 PSSMs corresponding to 7868 sequence and 2625 structural families. A RPS_BLAST interface allows sequence search against PSSMs of sequence or structural families or both. An analysis interface allows display and convenient navigation of alignments and domain hits.

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• SciCrunch
• 17 years ago - by Anonymous

A database dedicated to the analysis of gene expression and regulation data in Mycobacterium tuberculosis. It is designed to contain most of the characterized transcription start sites and DNA binding sites cross-referenced with their respective transcription factor, along with some predicted regulatory motifs.

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• SciCrunch
• 17 years ago - by Anonymous

A database of sequence-tagged sites (STSs) and a user interface for mapping partial deletions in the male-specific region of the human Y chromosome (MSY). Naturally occurring partial deletions in the human Y chromosome are associated with diverse phenotypes including male infertility, sex reversal, Turner syndrome, and germ cell tumor formation. With the complete sequence of the euchromatic Y chromosome in hand, it is now possible to precisely demarcate each deletion and the repertoire of genes lost, and to propose mechanisms of deletion. Detailed DNA-sequence analysis of MSY deletions is most readily accomplished with Y-specific STS assays, which employ the polymerase chain reaction (PCR). Each such STS assay provides a straightforward means of determining the presence or absence, in a sample of human genomic DNA, of a specific point along the length of the Y chromosome. In the course of analyzing normal and aberrant Y chromosomes over the past two decades, we and our colleagues have generated robust, Y-specific STSs at an average spacing of less than 14 kilobases across the MSY euchromatin. MSY Breakpoint Mapper provides information about these STSs and is useful for efficiently and systematically defining the breakpoint(s) of virtually any Y chromosome deletion.

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• SciCrunch
• 17 years ago - by Anonymous

A database of Arabidopsis mitochondrial protein import components. Detailed information can be found in two main areas of the website, one of which contains a diagram detailing the plant mitochondrial import process which users can click on and interact with, and the other containing information about arabidopsis mitochondrial protein import components.

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• SciCrunch
• 17 years ago - by Anonymous

A database containing information on ca. 4300 synthetic oligonucleotides with a sequence of up to 100 nucleotides. Data are mainly taken from the literature and are encoded on the basis of controlled vocabularies. The probes target 821 different genes, of which 691 human and 112 viral. The probes can be used for genetic polymorphisms study (1944), human inherited disease diagnosis (834), cancer diagnosis (517), infectious disease diagnosis (517), neurologic disease diagnosis (72), autoimmune disease diagnosis (40). Oligonucleotides are described on the basis of: name, oligo type (primer, probe, antisense), nucleotide sequence, amino acid sequence (if part of a coding region), target gene and related infos (localization within the gene and recognized variants or specificities), applications, methods, technical notes, complementary primer (if used for PCR), primers for amplification (if probe), bibliographic references. At the moment MPDB is searchable through some SRS servers. MPDB can easily be retrieved from our FTP server, together with SRS syntax files. Typology * ca. 4300 oligonucleotides * 821 different genes, of which 691 human and 112 viral * ca. 3536 oligonucleotides are human gene specific * ca. 620 oligonucleotides are viral gene specific

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• SciCrunch
• 17 years ago - by Anonymous

A resource for publicly available sequences of the rice genome(Specifically, Oryza sativa L.). Our goal at MOsDB is to provide all available data about rice genes and genomics, including (in the future) mutant information and expression profiles. At this moment, the MOsDB database includes current published sequences and gene annotation information of two Oryza sativa subspecies: japonica and indica. Rice is an experimental model for the cereal crops research and an agriculturally important plant, providing food for more than half of the world population. The estimated rice genome size is about 430 Mb, which is the smallest among all the cereal crops and about one seventh of human and 3.5 times of Arapdopsis genomes.

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• SciCrunch
• 17 years ago - by Anonymous