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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

A database dedicated to the comparative genomics of Mollicutes. Usual tools required to explore genomes have been infered in MolliGen. They include various ways to search for genes or groups of genes and to access to a wide range of related data. General information describing whole genome properties are also available as well as graphical representations. The genomic sequences deposited in MolliGen as well as related annotation data are inferred from the corresponding GenBank entries. The genomes implemented in MolliGen are all publicly accessible from general databases. Additionaly, some unpublished genomes can be deposited in MolliGen.

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• SciCrunch
• 17 years ago - by Anonymous

The database has been developed to structurally and functionally annotate, and where possible predict, the phenotypic consequences of mutations in protein kinases implicated in cancer. The 518 human protein kinases identified in KinBase, are listed alphabetically to facilitate browsing, and each gene is labelled with tumour type(s) in which mutations have been found. The list can also be sorted by selective pressure - the ratio of non-synonymous:synonymous mutations compared to that expected by chance, and by ''rank'' - the probability of the mutated gene containing at least 1 driver mutation. Both these measures can be used to predict which kinases contain driver mutations, i.e. those that are causal of the cancer, rather than passenger mutations that have arisen by chance but do not contribute to disease. Entries can be searched directly by gene name. Mutational data from the Cancer Genome Project have been mapped onto the crystal structures of the affected human protein domains where known, or onto the most closely related homologous structure if not known. Proteins are linked to functional annotation resources and are annotated with structural and functional features such as domains and phosphorylation sites, and protein interaction partners. This annotation is being expanded to include PROSITE patterns, which identify short peptide segments of functional consequence and sites of post-translation modifications, and Driver/Passenger assessment of the mutations.

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• SciCrunch
• 17 years ago - by Anonymous

A database of RNA modification pathways. The MODOMICS database contains the following types of items: * Modified Bases : Each modified base consists of a unique chemical structure. They are sorted by the regular RNA bases they originate from. The modified base queuosine is special, since it is synthesized first, and then attached to the ribose by a transglycosylation reaction. The letters in the small modification icons indicate what kingdoms of life the modifications occur in (Eukaryota, Archaea, EuBacteria, Mitochondria). In the download section, the .mol structure files for alare available. * Modification Pathways : Here, we present four pathway graphs showing what modifications emerge from the different bases. The letters in the small modification icons indicate what kingdoms of life the modifications occur in (Eukaryota, Archaea, EuBacteria, Mitochondria). All lines connecting two modifications are clickable, and show details on a particular reaction. * Enzymes : Lists enzymes that catalyse known reactions between modified bases. In the table, several alternatively used names for the enzymes are given, as well as a list of participating proteins. * Sequences : Shows sequences of RNAs with modifications highlighted. Currently, tRNAs and small and large subunit rRNAs are included in MODOMICS. * Publications : exactly that.

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• SciCrunch
• 17 years ago - by Anonymous

A database which supports high-throughput NMR and MS approaches to the identification and quantification of metabolites present in biological samples. MMCD serves as a hub for information on small molecules of biological interest gathered from electronic databases and the scientific literature. Each metabolite entry in the MMCD is supported by information in separate data fields, which provide the chemical formula, names and synonyms, structure, physical and chemical properties, NMR and MS data on pure compounds under defined conditions where available, NMR chemical shifts determined by empirical and/or theoretical approaches, calculated isotopomer masses, information on the presence of the metabolite in different biological species, and links to images, references, and other public databases. The MMCD search engine supports versatile data mining and allows users to make individual or bulk queries on the basis of experimental NMR and/or MS data plus other criteria.

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• SciCrunch
• 17 years ago - by Anonymous

A cross-platform (Windows/Mac/Unix) application that can display circular comparisons between a large number of genomes, with a focus on handling genome assembly data.

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• SciCrunch
• 13 years ago - by Anonymous

MolMovDB is a database that describes the motions that occur in proteins and other macromolecules, particularly using movies. Associated with it are a variety of free software tools and servers for structural analysis. The morph server enables the automatic generation of 2D and 3D animations of a plausible or semi-plausible pathway between two static conformations of a protein subunit, such as those conventionally solved by x-ray crystallography. We believe these animations and associated interpolated pathways will become a valuable research and educational tool, allowing the researcher or educator to quickly visualize the chemical transformation of a protein subunit from one conformation into another. With the server, it is easy to determine quickly whether a valid chemical pathway exists between two protein conformations, as in a protein such as calmodulin, or whether, as is the case with diphtheria toxin, the two conformations have no clearly valid chemical pathway and therefore exist most likely as the result of other processes, such as domain swapping.

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• SciCrunch
• 17 years ago - by Anonymous