Curator Dashboard

ProPortal is a database containing genomic, metagenomic, transcriptomic and field data for the marine cyanobacterium Prochlorococcus. Our goal is to provide a source of cross-referenced data across multiple scales of biological organization--from the genome to the ecosystem--embracing the full diversity of ecotypic variation within this microbial taxon, its sister group, Synechococcus and phage that infect them. The site currently contains the genomes of 13 Prochlorococcus strains, 11 Synechococcus strains and 28 cyanophage strains that infect one or both groups. Cyanobacterial and cyanophage genes are clustered into orthologous groups that can be accessed by keyword search or through a genome browser. Users can also identify orthologous gene clusters shared by cyanobacterial and cyanophage genomes. Gene expression data for Prochlorococcus ecotypes MED4 and MIT9313 allow users to identify genes that are up or downregulated in response to environmental stressors. In addition, the transcriptome in synchronized cells grown on a 24-h light-dark cycle reveals the choreography of gene expression in cells in a ''natural'' state. Metagenomic sequences from the Global Ocean Survey from Prochlorococcus, Synechococcus and phage genomes are archived so users can examine the differences between populations from diverse habitats. Finally, an example of cyanobacterial population data from the field is included.

• Resource
• SciCrunch
• 15 years ago - by Anonymous

Software for gene prediction in eukaryotic genomic sequences. Serves as a basis for further steps in the analysis of sequenced and assembled eukaryotic genomes.

• Resource
• SciCrunch
• 17 years ago - by Anonymous

Portal for deposition and retrieval of cryo electron microscopy (3DEM) density maps, atomic models, and associated metadata. Global resource for 3 Dimensional Electron Microscopy structure data archiving and retrieval, news, events, software tools, data standards, validation methods.

• Resource
• SciCrunch
• 17 years ago - by Anonymous

A web server that classifies proteins into two classes from their sequences alone: the membrane protein class and the non-membrane protein class. This may be important in the functional assignment and analysis of open reading frames (ORF''s) identified in complete genomes and, especially, those ORF''s that correspond to proteins with unknown function. The network has a simple hierarchical feed-forward topology and a limited number of neurons which makes it very fast. By using only information contained in 11 protein sequences, the method was able to identify, with 100% accuracy, all membrane proteins with reliable topologies collected from several papers in the literature. Applied to a test set of 995 globular, water-soluble proteins, the neural network classified falsely 23 of them in the membrane protein class (97.7% of correct assignment). The method was also applied to the complete SWISS-PROT database with considerable success and on ORF''s of several complete genomes. The neural network developed was associated with the PRED-TMR algorithm (Pasquier,C., Promponas,V.J., Palaios,G.A., Hamodrakas,J.S. and Hamodrakas,S.J., 1999) in a new application package called PRED-TMR2.

• Resource
• SciCrunch
• 15 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.

• Resource
• SciCrunch
• 13 years ago - by Anonymous

A cross-database search service for Drosophila gene expression data, including microarray data from FlyAtlas and in situ images from BDGP and Fly-TED. The applications provide different ways to search for and compare gene expression data for the fruit fly Drosophila melanogaster. You may Search Gene Expression Data by Gene, Gene Batch, and by Tissue Expression Profile. A number of Web services (SPARQL endpoints) are provided from this site which may be queried programmatically for data.

• Resource
• SciCrunch
• 16 years ago - by Anonymous

A database for aligned ribosomal complexes that provides a resource for directly comparing the structures. A collection of files deposited in the RCSB protein data bank and the Electron Microscopy Data Bank have been aligned so as to make direct comparison of the structures possible. An easy-to-use, searchable interface allows users to access and download >130 cryo-EM maps and >300 atomic models in the format of brix and pdb files, respectively. The aligned coordinate system substantially simplifies direct visualization of conformational changes in the ribosome, such as subunit rotation and head-swiveling, as well as direct comparison of bound ligands, such as antibiotics or translation factors.

• Resource
• SciCrunch
• 15 years ago - by Anonymous

Software program for clustering large number of short similar DNA sequences. It was originally designed for clustering targeted 16S rRNA pyrosequencing reads.

• Resource
• SciCrunch
• 13 years ago - by Anonymous

RANDOM.ORG is a true random number service that generates randomness via atmospheric noise. This page explains why it''s hard (and interesting) to get a computer to generate proper random numbers. Random numbers are useful for a variety of purposes, such as generating data encryption keys, simulating and modeling complex phenomena and for selecting random samples from larger data sets. They have also been used aesthetically, for example in literature and music, and are of course ever popular for games and gambling. When discussing single numbers, a random number is one that is drawn from a set of possible values, each of which is equally probable, i.e., a uniform distribution. When discussing a sequence of random numbers, each number drawn must be statistically independent of the others. With the advent of computers, programmers recognized the need for a means of introducing randomness into a computer program. However, surprising as it may seem, it is difficult to get a computer to do something by chance. A computer follows its instructions blindly and is therefore completely predictable. (A computer that doesn''t follow its instructions in this manner is broken.) There are two main approaches to generating random numbers using a computer: Pseudo-Random Number Generators (PRNGs) and True Random Number Generators (TRNGs). The approaches have quite different characteristics and each has its pros and cons.

• Resource
• SciCrunch
• 17 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.

• Resource
• SciCrunch
• 16 years ago - by Anonymous

Flexible barcode and adapter removal for sequencing platforms.

• Resource
• SciCrunch
• 13 years ago - by Anonymous

Collates and curates neuroanatomical data and information generated both in-house and by community to communicate current state of knowledge about neuroanatomical structures in developing zebrafish. Most of data come from high resolution confocal imaging of intact brains in which neuroanatomical structures are labelled by combinations of transgenes and antibodies. Community repository for image based data related to neuroanatomy of zebrafish.

• Resource
• SciCrunch
• 15 years ago - by Anonymous

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 2, 2025. Database of chemicals and reactions inside of US patents (2001 - 2011). SCRIPDB provides the full original patent text, reactions and relationships described within any individual patent, in addition to the molecular files common to structural databases. The patent literature is a rich catalog of biologically relevant chemicals; many public and commercial molecular databases contain the structures disclosed in patent claims. However, patents are an equally rich source of metadata about bioactive molecules, including mechanism of action, disease class, homologous experimental series, structural alternatives, or the synthetic pathways used to produce molecules of interest. Unfortunately, this metadata is discarded when chemical structures are deposited separately in databases. SCRIPDB is a chemical structure database designed to make this metadata accessible. The SCRIPDB information is valuable in medical text mining, chemical image analysis, reaction extraction and in silico pharmaceutical lead optimization. SCRIPDB may be searched by exact chemical structure, substructure or molecular similarity and the results may be restricted to patents describing synthetic routes.

• Resource
• SciCrunch
• 15 years ago - by Anonymous

Software tool that enables analysis of RNA-seq data with or without reference genome. Local transcriptome assembler for SNPs, indels and AS events.

• Resource
• SciCrunch
• 13 years ago - by Anonymous

A virtual database of several model resources including: CellML Model Repository, ModelDB, Open Source Brain, SimTK, and ModelRun.

• Resource
• SciCrunch
• 14 years ago - by Anonymous

The Bioinformatics, Algorithmics, and Data Mining group BIIT lead by prof. Jaak Vilo is a joint research group between the Department of Computer Science (University of Tartu), Quretec, and the Estonian Biocenter. Our main research topics and capabilities include the gene regulation, gene expression data analysis, biological data mining, systems biology, combinatorial pattern matching, developing software for biomedical research databases, as well as partnering in stem cell and cancer related projects. Software * MEM - Multi-Experiment-Matrix -- large-scale gene expression data queries and mining (Genome Biology 2009) * g:Profiler family of tools for functional assessment of gene groups, gene ID mappings, orthology and expression similarity searches. (NAR web server issue 2007) * KEGGanim - visualisation of high-throughput data on biological pathway charts (Bioinformatics, 2007) * GraphWeb - a tool for mining large biological networks (NAR Web server issue 2008) * FunGenES data atlas * More software tools

• Resource
• SciCrunch
• 15 years ago - by Anonymous

Software for tracking and quantifying DNA damage patterns among ancient DNA sequencing reads generated by Next-Generation Sequencing platforms.

• Resource
• SciCrunch
• 13 years ago - by Anonymous

A nonprofit organization dedicated to providing an international forum for the latest scientific discoveries, medical practices and caregiver initiatives related to Parkinson's disease. It hosts the annual World Parkinson Congress, an event which focuses on bringing physicians, scientists, allied health professionals, caregivers and people diagnosed with Parkinson's disease together, in order to create a global dialogue that will help expedite treatment practices and the discovery of a cure .

• Resource
• SciCrunch
• 17 years ago - by Anonymous

Software application that is part of the LINKAGE auxiliary programs (entry from Genetic Analysis Software)

• Resource
• SciCrunch
• 14 years ago - by Anonymous

Software package for signal-level analysis of Oxford Nanopore sequencing data.

• Resource
• SciCrunch
• 9 years ago - by Anonymous