Curator Dashboard

A web based graphical tool for exploring gene structure of the human genome, including alternative splicing. It is based on a mapping of the EST consensus sequences (contigs) from GeneNest to the complete human genome. SpliceNest is integrated with GeneNest and the SYSTERS protein sequence cluster set in one framework, permitting an overall exploration of the whole sequence space covering protein, mRNA and EST sequences, as well as genomic DNA. Users can search for alignments by browsing, utilizing the graphical chromosome display feature, or performing a cluster, keyword or BLAST search.

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• SciCrunch
• 17 years ago - by Anonymous

A database containing compound microsatellite-SNP markers in human, dog, mouse, rat and chicken. SNPSTRs are a relatively new type of compound genetic marker which combines a STR marker with one or more tightly linked SNPs. This combination of co-inherited markers evolving at different rates may offer the possibility of gaining better resolved insights into population genetic processes compared to when these different marker types are used separately. SNPSTRs were first described by Mountain et al (2002) who developed experimental protocols for autosomal SNPSTRs which contain a SNP and a microsatellite within 500 base pairs apart. microsatellite-SNP, dog microsatellite-SNP, mouse microsatellite-SNP, rat microsatellite-SNP, chicken microsatellite-SNP

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• SciCrunch
• 17 years ago - by Anonymous

The ExPASy (Expert Protein Analysis System) proteomics server of the Swiss Institute of Bioinformatics (SIB) is dedicated to the analysis of protein sequences and structures as well as 2-D PAGE. It is a curated protein sequence database which strives to provide a high level of annotation, a minimal level of redundancy and high level of integration with other databases. Recent developments of the database include format and content enhancements, cross-references to additional databases, new documentation files and improvements to TrEMBL, a computer-annotated supplement to SWISS-PROT.

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• SciCrunch
• 17 years ago - by Anonymous

It provides a central resource for sequence verification of SNPs. The goal of the SNP500Cancer project is to resequence 102 reference samples to find known or newly discovered single nucleotide polymorphisms (SNPs) which are of immediate importance to molecular epidemiology studies in cancer. The site allows users to search for SNPs using SNP identifier, gene symbol, gene alias, chromosome location, or gene ontology pathway.

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• SciCrunch
• 17 years ago - by Anonymous

Biomedical technology research center that (1) exploits the budding yeast Saccharomyces cerevisiae to develop novel technologies for investigating and characterizing protein function and protein structure (2) facilitates research and extension of new technologies through collaboration, and (3) actively disseminates data and technology to the research community. Through collaboration, the YRC freely provides resources and expertise in six core technology areas: Protein Tandem Mass Spectrometry, Protein Sequence-Function Relationships, Quantitative Phenotyping, Protein Structure Prediction and Design, Fluorescence Microscopy, Computational Biology.

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• SciCrunch
• 17 years ago - by Anonymous

A database for human SNPs (single nucleotide polymorphisms) that result in PTCs (premature termination codons) and trigger nonsense-mediated mRNA decay (NMD). The SNP2NMD interfaces provide extensive genetic information on and graphical views of the queried SNP, gene, and disease terms.

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• SciCrunch
• 17 years ago - by Anonymous

SNP at Ethnos is a catalog of human SNPs and genes that contain human ethnic variation. The database contains the following results for detecting natural selection and population difference: * Neareast Shrunken Centroid Method Score for detecting ethnic difference * Fst * Hudson, Kreitman and Aguade (HKA) test (1987) * Tajima''''s D test (1989) * Fu and Li D test (1993) It also contains copious links to dbSNP, Entrez Gene, GeneCards, OMIM, HGMD, International HapMap SNP at domain, and Haplotter (EHH). You can search by entering a gene symbol or an rs number in the text box at Data Search page. Search results provide above selection analysis data, rs lists corresponding a searched gene, and a genome viewer which contains functional annotation. The data underlying these analyses are from the Phase I HapMap Project.

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• SciCrunch
• 15 years ago - by Anonymous

This is a database of human C/D box and H/ACA modification guide RNAs. Information on a particular snoRNA can be accessed by three ways: 1- On the Search page, just type the name of the snoRNA (for example ACA17) in the Id window. 2- The Find guide RNA contains the sequences of the human ribosomal rRNAs 28S, 18S and 5.8S, and of the snRNAs U1, U2, U4, U5 and U6, with the positions of modified (2''O-ribose methylated or pseudo-uridinylated) nucleotides, and the identity of the corresponding modification guide RNAs. You can click on the name of the relevant snoRNA. 3- By utilizing the link to the UCSC Human Genome Browser.

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• SciCrunch
• 17 years ago - by Anonymous

A curated database for small nucleolar RNAs and small cajal body-specific RNAs. It presents sno/scaRNA-associated genetic and functional data and provides access to several other database sources via web-accessible search interfaces. Consisting of 1979 sno/scaRNA records obtained from 85 organisms, sno/scaRNAbase is a combination of systematic literature curation and annotation effort. small nucleolar RNA, small cajal body-specific RNA

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• SciCrunch
• 17 years ago - by Anonymous

An object-oriented database of domain-domain interactions observed in structural data. SNAPPI-DB is a useful resource for any analysis of structures but has been opitmised for analysis on domain-domain interactions and domain-ligand interactions. The database has already been employed for 3 studies on the properties of domain-domain interactions and is currently being employed to train a protein-protein interaction predictor and a functional residue predictor. SNAPPI-DB has several features which are not available in other databases, including links to the MSD, speed, being object oriented, storage of multiple domain definitions, and storage of Protein Quaternary Structures (PQS).

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• SciCrunch
• 17 years ago - by Anonymous

A sequence analysis tool providing a simple but detailed analysis of human genes and their variations. For each gene, a gene-gene relationship network can be generated based on protein-protein interaction data, metabolic pathway connections and extended through phylogenetic relations. Snap provides tools for designing sequence primers and evaluating RNA splicing effects of single SNPs - known from the databases or defined by you. Primers can be designed for the amplification or sequencing of cDNA, genomic DNA, introns only or exons only., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

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• SciCrunch
• 17 years ago - by Anonymous

A free software tool to identify length variation of microsatellites from short sequence reads.

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• SciCrunch
• 13 years ago - by Anonymous

A database that integrates all available data associated with the planarian genome, including predicted and annotated genes, ESTs, protein homologies, gene expression patterns and RNAi phenotypes. It is GMOD compliant. The planarian Schmidtea mediterranea is rapidly emerging as a key model organism for the study of regeneration, tissue homeostasis and stem cell biology. Thus, SmedGD features a genome browser, BLAST capability, and other search options in order to facilitate the advancement of scientific knowledge of this organism.<

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• SciCrunch
• 17 years ago - by Anonymous

The SKY/M-FISH and CGH databases provide a public platform for investigators to share and compare their molecular cytogenetic data. The database is open to everyone and all users can view an individual investigator&apos;s public data or compare public cases from different investigators. Those wishing to contribute their own data must register and can choose to keep their data private for a period not to exceed two years. Spectral Karyotyping (SKY), Multiplex Fluorescence In Situ Hybridization (M-FISH) and Comparative Genomic Hybridization (CGH) are complementary fluorescent molecular cytogenetic techniques. SKY/M-FISH permits the simultaneous visualization of each human or mouse chromosome in a different color, facilitating the identification of chromosomal aberrations. CGH utilizes the hybridization of differentially labeled tumor and reference DNA to generate a map of DNA copy number changes in tumor genomes.

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• SciCrunch
• 17 years ago - by Anonymous

THIS RESOURCE IS NO LONGER IN SERVICE, documented August 22, 2016. A database of known ligand binding sites within the PDB which is navigable by PDB identifier or ligand 3 letter code e.g. NAD. Each binding site has a frequently updated register of structurally similar binding sites sharing atomic similarity detected by geometric hashing. Multiple alignments, structural superpositions and links to other structural databases are also available enabling further analysis. The rapid expansion of structural information for protein-ligand binding sites is potentially an important source of information in structure-based drug design and in understanding ligand cross reactivity and toxicity. We have developed a large database of ligand binding sites extracted automatically from the Protein Data Bank. This has been combined with a method for calculating binding site similarity based on geometric hashing to create a relational database for the retrieval of site similarity and binding site superposition. It contains an all-against-all comparison of binding sites and holds known protein-ligand binding sites, which are made accessible to data mining. Here we demonstrate its utility in two structure-based applications: in determining site similarity and in aiding the derivation of a receptor-based pharmacophore model.

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• SciCrunch
• 17 years ago - by Anonymous

Data analysis service to predict the functional consequences of known and unknown variants.

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• SciCrunch
• 13 years ago - by Anonymous

THIS RESOURCE IS NO LONGER IN SERVICE, documented on July 15, 2013. A collection of manually curated protein structural alignments and their interrelationships. Each multiple alignment within the SISYPHUS database consists of structurally similar regions common to a group of proteins. These regions range from oligomeric biological units, or individual domains to fragments of different size representing either internal structural repeats or motifs common to structurally distinct proteins. The SISYPHUS multiple alignments are displayed with SPICE, a browser that provides an integrated view of protein sequences, structures and their annotations.

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• SciCrunch
• 17 years ago - by Anonymous

This is a site with links to several siRNA services, including siRNA base sequence searches, specificity searches, known siRNA molecule searches, and target sequences. One of the sites, called siSVM, allows users to predict efficacy of siRNAs given their base sequence using features derived from the siRNA sequence. siSVM is designed to allow common methods of siRNA design to be included in the search. This includes motif rules,energy conditions and specificity searching. The second site it links to, siRNA specificity prediction, allows users to perform a specificity search for siRNAs to avoid off-target effects. SpecificityServer is designed to help you identify potential non-specific matches to your siRNA. It incorporates the latest information about non-specific matches (sequence-specific only). The third site it links to, siRNAdb, is a database of known siRNA molecules. It provides a list of sirnaID, target, geneID, geneAcc, TargetStart, and targetEnd.Category: RNA sequence databases

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• SciCrunch
• 17 years ago - by Anonymous

On this site, you can search siRNA records, design siRNAs, or submit siRNA records resulting from your own study (requires register/login). Small interfering RNAs (siRNAs) are a class of 20-25 nucleotide-long double-stranded RNAs, and they are widely used as gene knock-down tool in molecular genetics, functional genomics, and drug discovery studies. However, despite numerous efforts, the design of potent siRNA remains inadequate. Design rules resulting from different studies often disagree with each other, and are often unsatisfactory. Typically, only about 75-80% siRNAs designed based on current rules result in &gt;50% knock-down efficacy. Observing these difficulties, we have established this database of experimentally validated mammalian siRNAs with efficacy ratings. As of August 18, 2008, 17,192 records of experimentally validated siRNAs, targeting 5,086 genes, originated from 6,122 independent studies are hosted in siRecords.

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• SciCrunch
• 17 years ago - by Anonymous

It provides a database based on a pre-computed similarity matrix covering the similarity space formed by &gt;4 million amino acid sequences from public databases and completely sequenced genomes. The database is capable of handling very large datasets and is updated incrementally. For sequence similarity searches and pairwise alignments, we implemented a grid-enabled software system, which is based on FASTA heuristics and the Smith Waterman algorithm. SimpleSIMAP and AdvancedSIMAP retrieve homologs for given protein sequences that need to be contained in the SIMAP database. While SimpleSIMAP provides only selected parameters and preconfigured search spaces, the AdvancedSIMAP allows the user to specify search space, filtering and sorting parameters in a flexible manner. Both types of queries result in lists of homologs that are linked in turn to their homologs. So the web interfaces allow users to explore quickly and interactively the protein world by homology. Sponsors: SIMAP is supported by the Department of Genome Oriented Bioinformatics of the Technische Universitt Mnchen and the Institute for Bioinformatics of the GSF-National Research Center for Environment and Health.

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• SciCrunch
• 14 years ago - by Anonymous