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TomatEST DB is a collection of tomato EST sequences downloaded from dbEST. Gene indices are created by grouping overlapping EST sequences into clusters. Each cluster corresponds to a unique gene. A cluster can consist in one or multiple contigs. In the case of a cluster of multiple contigs each contig share similarities with the others in the cluster because of i) putative alternative transcription; ii) paralogy; iii) domain sharing.

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• SciCrunch
• 17 years ago - by Anonymous

THIS RESOURCE IS NO LONGER IN SERVICE, documented August 24, 2017.<br/><br/>Platform to enable dissemination of scientific findings, foster open peer commentary and promote collaboration among the research community. Widespread participation in OneLab will increase the quality, transparency and reproducibility of data thus accelerating the pace of scientific discoveries. The result will be a streamlined process from the bench to the clinic with tremendous benefits for the well-being of the general public. OneLab is a private professional network that mirrors the hierarchy of real world research laboratories. Users are designated as either principal investigators (PI) or lab members. PIs can invite lab members to join and data posted by lab members cannot be shared without PI approval. In this way the PI retains FULL CONTROL over the dissemination of scientific content thus safeguarding the primacy of authorship. This professional network will serve as a backdrop for sharing scientific findings, promote collaborations, and provide a basis for open peer commentary. Semantic Search of Structured Content OneLab implements a powerful search functionality that is based on structured content. Users describe their Single Figure Posts (SFPs) using defined fields such as model organism, genes, proteins and assay. This additional layer of structure provides the basis for a smarter and more accurate search engine that understands searcher intent and therefore generates more relevant results. Structured content allows OneLab to go one step further by offering recommendations based on similarities that might not be intuitive, thus increasing potential collaborations among scientists., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

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• SciCrunch
• 15 years ago - by Anonymous

Phospho3D is a database of three-dimensional structures of phosphorylation sites which stores information retrieved from the phospho.ELM database and which is enriched with structural information and annotations at the residue level. The database also collects the results of a large-scale structural comparison procedure providing clues for the identification of new putative phosphorylation sites.

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• SciCrunch
• 17 years ago - by Anonymous

BioOntology.ch is a blog on the interlinked bio-ontologies for knowledge-based data-driven science. * Bio-ontology is standards: Modern research generates data at unprecedented rates. Where such data are described and labelled using unconstrained text, different terminology is often used for similar or identical things. Such terminological variance is normal and reflects natural language; usually humans have no difficulty resolving ambiguous usages of terminology and discrepant labels. However, due to the sheer volumes of research data being generated, it is necessary to develop computational methods of aggregating and aligning like with like. One approach to addressing this issue is to adopt shared standards for the categorisation of data. Agreement in annotation across different databases increases the value of a standardised terminology, allowing for easier cross-domain integration and querying. * Bio-ontology is knowledge representation: Modern biomedical ontologies harness the formal semantics underlying the Web Ontology Language (OWL), which allows complex logical expressions to be built that define knowledge about the domain, in such a fashion that computers can perform automatic reasoning for tasks such as hierarchy management and consistency checking / error detection. OWL is based on Description Logics, a family of decidable logical languages optimised for the expression of large-scale terminological knowledge such as is found within large biomedical vocabularies. * Bio-ontology is interdisciplinarity: Increasingly, research in the life sciences needs to integrate knowledge and results from multiple disparate fields and methodological approaches in order to gain insight into underlying biological mechanisms. This is the case, for example, when studying the genetic and epigenetic factors in understanding behavioural phenotypes, or in the development of predictive models to enable personalised and translational medicine. Research results from diverse disciplines such as genetics, molecular biology, physiology, chemistry, psychology and medicine have to be integrated in order to build a coherent picture of what is known in order to address key research gaps.

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• SciCrunch
• 15 years ago - by Anonymous

A Brachypodium distachyon comparative genomics resource offering a genome browser, BLAST server, download capabilities, Brachypodium physical map, Comparative maps, and comparison with rice and Sorghum chromosomes. * Genome browser >>> Browse the v1.0 genome assembly and the v1.0 gene predictions from JGI/MIPS. Also displays JIC FST data (T-DNA lines) and alignments of ESTs from wheat, barley and Brachypodium. * BLAST server >>> BLAST your sequences against the Brachypodium sequence assembly and the predicted proteome. * Download sequence >>> Download sequence from the brachy assembly (limited to 50kb regions). Download complete assembly file as FASTA. Download sequence and additional data from the v1.0 annotated assemblyincluding protein-coding sequences as FASTA, translated coding sequences as FASTA, gene sequences as FASTA, and COS markers. PLEASE NOTE: The published genome analysis is based on the v1.0 annotation. The v1.2 annotation can be downloaded from MIPS. * Brachypodium physical map >>> Brachypodium physical map data displayed using SyMAP. (view in genome browser) * Comparative maps >>> Brachypodium genetic and physical maps aligned to rice and wheat. * Comparison with rice and Sorghum chromosomes >>> Dotplots of the Brachypodium assembly aligned to rice and Sorghum chromosomes.

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• SciCrunch
• 15 years ago - by Anonymous

A software program to identify artificial duplicates from raw 454 sequencing reads, including exact duplicates and near identical duplicates.

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• SciCrunch
• 13 years ago - by Anonymous

The tmRDB is a tool in the study of the structures and functions of the tmRNA (earlier called 10S RNA). As the name implies, tmRNA has properties of tRNA and mRNA combined in a single molecule. The tmRDB provides aligned, annotated and phylogenetically ordered tmRNA sequences. The alignments of the sequences represent conserved secondary structure elements where each base pair is proven by comparative sequence analysis. Where possible, we established direct links to primary sources. We acknowledge support provided by the National Institutes of Health and the Danish Technical Research Council. tRNA, mRNA, trans-translation, rescue, ribosome, broken mRNA, bacteria, mitochondria chloroplasts, cyanelles, bacteriphage, phylogenetic

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• SciCrunch
• 17 years ago - by Anonymous

Software that provides a simple way to do some quality control checks on raw sequence data coming from high throughput sequencing pipelines.

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• 13 years ago - by Anonymous

A collection of amino acid sequences for all the completed genomes and the annotated trans beta-barrel membrane proteins (TMBs) using different discrimination algorithms. For each genome, the calculations have been performed with statistical methods and machine learning techniques and the results are accumulated in the database. TMBETA-GENOME has the feasibility of selecting the organism from the three kingdoms of life, archaea, bacteria and eukaryote. Further, users have the option to select any of the methods or their combinations, and display the results with/without amino acid sequence information.

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• SciCrunch
• 17 years ago - by Anonymous

The mission of AIDS.ORG is to help prevent HIV infections and to improve the lives of those affected by HIV and AIDS by providing education and facilitating the free and open exchange of knowledge at an easy-to-find centralized website. AIDS.ORG makes access to important AIDS information easier and faster. We provide prevention, testing, and treatment information currently to well over 4 million people a year. AIDS.ORG has been awarded the Health on the Net Foundation Code of Conduct (HONcode) seal for reliability and credibility of information in the field of healthcare. Additionally, every year over 2.4 million young people under the age of 25 turn to AIDS.ORG, making us an important resource since over 50% of all new HIV infections in the USA occur in this age group. AIDS.ORG, Inc. is a nonprofit 501(c) (3) educational organization, and maintains a very strict privacy policy. We make it our goal to be the best starting point for someone looking for AIDS information on the Internet. Our intent is that users be directed to the best information on the topic they''re investigating. We bring people together to share knowledge and experiences. In the past, we also provided the very first Internet-based program of accredited AIDS education for medical professionals, allowing doctors in rural and isolated areas to better serve AIDS patients.

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• SciCrunch
• 15 years ago - by Anonymous

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 2nd,2023. TMAD stores raw and processed data from Tissue Microarray experiments along with their corresponding stained tissue images. In addition, TMAD provides methods for data retrieval, grouping of data, analysis and visualization as well as export to standard formats. Researchers at the Stanford University School of Medicine and their collaborators worldwide have constructed many tissue microarrays for use in basic research.

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• SciCrunch
• 17 years ago - by Anonymous

An Software resource

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• SciCrunch
• 13 years ago - by Anonymous

Software tool as collection of command line tools for Short-Reads FASTA/FASTQ files preprocessing.

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• SciCrunch
• 13 years ago - by Anonymous

How do the recent developments in neuroscience affect psychology and society? Today, many new findings challenge the way we think about ourselves and others. These changes impact on how we should think about issues such as the self, mentality, psychology, free will, morale, law and society. Through interviews of prominent scholars in the fields of neuroscience and beyond, the BrainEthics Podcast provides updated, novel and comprehensive news and views from the world of neuroscience, and how the world responds to it. We provide a full list of all podcast episodes. Although we are hosting all episodes, you can also subscribe to the podcast on all major podcasting directories.

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• SciCrunch
• 15 years ago - by Anonymous

Ministry of Higher Education, Research and Innovation, France is one of the 900 Higher Education-related Organizations and Associations.

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• SciCrunch
• 13 years ago - submitted by Andrea Stagg

Open source software tool to merge paired-end reads from next-generation sequencing experiments. Designed to merge pairs of reads when original DNA fragments are shorter than twice length of reads. Can improve genome assemblies and transcriptome assembly by merging RNA-seq data.

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• SciCrunch
• 13 years ago - by Anonymous

There are a lot of fine blogs out there covering the avalance of current neuroscience research. With this blog Thomas Rams��y & Martin Skov want to highlight the many consequences of this growing understanding of the human brain. We are especially interested in two types of consequences: Tinkering with the brain and What is it like to be a human being? * Tinkering with the brain: First and foremost, with an understanding of how the brain works comes the possibility of tinkering with it. We already use billions of dollars every year on psychopharmocologia trying to treat depression, schizophrenia, obsessive-compulsive disorder and other mental diseases. But should we also use our knowledge of the brain to treat undesirable mental traits such as pedophilia or sociopathy? And what about enhancing normal brains? Clearly, evolution hasn''t endowed us with the most efficient brain imaginable. Shouldn''t we do something about its many shortcomings? * What is it like to be a human being?: Secondly, our view of human behavior is sure to change with our improved understanding of the human brain. Our knowledge of core human faculties such as language, social reasoning, aesthetics, and economics is already being challenged by modern neuroscience, yielding multiple hard questions. Do we have a free will? Is the mind innate or plastic? If people are not responsible for their actions (since all actions are caused by blind molecular processes) does our legal system still make sense? In short, will modern neuroscience come to completely redefine human nature? We try to discuss contemporary research literature, not just news reports. Although we will occasionally also target popular science reports, since we believe they play an important role in dissemining lessons from the lab. And in the future we plan to also post interviews with interesting researchers, as well as link to our own publications in journals and books. Additionally, the latest and most important books in the multidisciplinary field of neuroscience, cognition, psychology, ethics and economics are presented.

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• SciCrunch
• 15 years ago - by Anonymous

Database for identifying orthologous phenotypes (phenologs). Mapping between genotype and phenotype is often non-obvious, complicating prediction of genes underlying specific phenotypes. This problem can be addressed through comparative analyses of phenotypes. We define phenologs based upon overlapping sets of orthologous genes associated with each phenotype. Comparisons of >189,000 human, mouse, yeast, and worm gene-phenotype associations reveal many significant phenologs, including novel non-obvious human disease models. For example, phenologs suggest a yeast model for mammalian angiogenesis defects and an invertebrate model for vertebrate neural tube birth defects. Phenologs thus create a rich framework for comparing mutational phenotypes, identify adaptive reuse of gene systems, and suggest new disease genes. To search for phenologs, go to the basic search page and enter a list of genes in the box provided, using Entrez gene identifiers for mouse/human genes, locus ids for yeast (e.g., YHR200W), or sequence names for worm (e.g., B0205.3). It is expected that this list of genes will all be associated with a particular system, trait, mutational phenotype, or disease. The search will return all identified model organism/human mutational phenotypes that show any overlap with the input set of the genes, ranked according to their hypergeometric probability scores. Clicking on a particular phenolog will result in a list of genes associated with the phenotype, from which potential new candidate genes can identified. Currently known phenotypes in the database are available from the link labeled ''Find phenotypes'', where the associated gene can be submitted as queries, or alternately, can be searched directly from the link provided.

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• SciCrunch
• 15 years ago - by Anonymous

This blog highlights and comments on current research and hypotheses relating to how the brain wires itself up during development, how the end result can vary in different people and what happens when it goes wrong. It includes discussions of the genetic and neurodevelopmental bases of traits such as intelligence and personality characteristics, as well as of conditions such as schizophrenia, autism, dyslexia, epilepsy, synaesthesia and others.

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• SciCrunch
• 15 years ago - by Anonymous

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 2nd,2023. TMAD stores raw and processed data from Tissue Microarray experiments along with their corresponding stained tissue images. In addition, TMAD provides methods for data retrieval, grouping of data, analysis and visualization as well as export to standard formats. Researchers at the Stanford University School of Medicine and their collaborators worldwide have constructed many tissue microarrays for use in basic research.

• Resource
• SciCrunch
• 17 years ago - by Anonymous