Curator Dashboard

A web tool for prediction of signal peptides in archaea. Computational prediction of signal peptides (SPs) and their cleavage sites is of great importance in computational biology; however, currently there is no available method capable of predicting reliably the SPs of archaea, due to the limited amount of experimentally verified proteins with SPs. We performed an extensive literature search in order to identify archaeal proteins having experimentally verified SP and managed to find 69 such proteins, the largest number ever reported. A detailed analysis of these sequences revealed some unique features of the SPs of archaea, such as the unique amino acid composition of the hydrophobic region with a higher than expected occurrence of isoleucine, and a cleavage site resembling more the sequences of gram-positives with almost equal amounts of alanine and valine at the position-3 before the cleavage site and a dominant alanine at position-1, followed in abundance by serine and glycine. Using these proteins as a training set, we trained a hidden Markov model method that predicts the presence of the SPs and their cleavage sites and also discriminates such proteins from cytoplasmic and transmembrane ones.

• Resource
• SciCrunch
• 15 years ago - by Anonymous

Software ultrafast memory efficient tool for aligning sequencing reads. Bowtie is short read aligner.

• Resource
• SciCrunch
• 13 years ago - by Anonymous

Wikikidney.org is an effort to prevent kidney diseases and achieve better outcomes in those who have end stage renal disease. Our mission is to use this medium to make the public more aware of kidney disease in a sincere effort to prevent it when we can, and to help our colleagues achieve good outcomes in those who already have end stage renal disease. Our role is to provide as much information as possible to patients, professionals and the general public, with the hopes that this education will be a motivating factor in making the necessary changes to prevent or stall chronic kidney disease. After nearly two decades of seeing patients with end stage renal disease, it is apparent that much of what we deal with can be delayed or prevented altogether. Several medical trials and innovations in the last several years have confirmed these observations, and form the basis of this website. A major element in preventing renal illness is simply early detection, and for this one needs education. As the Internet expands and becomes more and more a tool of everyday life, we will have the ability to access and distribute information like no other generation before us. Qualified readers are encouraged to contribute to existing articles and to create articles of their own. Contents * 1 Kidney Resources - NIC * 2 Especially for Patients * 3 General Kidney Resources * 4 Issues in Nephrology * 5 Clinical Wiki Projects * 6 Be an author, editor or reviewer on wikikidney * 7 Clinical Trials * 8 Newsdesk Top Stories * 9 Essential Physician Resources * 10 Organizations * 11 Government Agencies * 12 Vendor and other Sites * 13 Patents * 14 Index

• Resource
• SciCrunch
• 16 years ago - by Anonymous

Blog by Brian E. Moore, MD, discussing issues pertaining to the practice of neuropathology -- including nervous system tumors, neuroanatomy, neurodegenerative disease, muscle and nerve disorders, ophthalmologic pathology, neuro trivia, neuropathology gossip, job listings and anything else that might be of interest to a blue-collar neuropathologist. Brian E. Moore, MD: Neuropathologist, Memorial Medical Center in Springfield, Illinois. Co-Chair, Southern Illinois University School of Medicine Department of Pathology.

• Resource
• SciCrunch
• 15 years ago - by Anonymous

A software toolkit for tandem mass spectrometry analysis, with a focus on peptide identification. Crux analyzes shotgun proteomics tandem mass spectra, associating peptides with observed spectra. This software toolkit for tandem mass spectrometry analysis, with a focus on peptide identification is provided as a single executable. Crux is implemented in C and is distributed with source code freely to noncommercial users. Mass spectrometry, the core technology in the field of proteomics, promises to enable scientists to identify and quantify the entire complement of proteins in a complex biological sample. Currently, the primary bottleneck in this type of experiment is computational. Existing algorithms for interpreting mass spectra are slow and fail to identify a large proportion of the given spectra. We describe a database search program called Crux that reimplements and extends the widely used database search program Sequest. For speed, Crux uses a peptide indexing scheme to rapidly retrieve candidate peptides for a given spectrum. For each peptide in the target database, Crux generates shuffled decoy peptides on the fly, providing a good null model and, hence, accurate false discovery rate estimates. Crux also implements two recently described postprocessing methods: a p value calculation based upon fitting a Weibull distribution to the observed scores, and a semisupervised method that learns to discriminate between target and decoy matches. Both methods significantly improve the overall rate of peptide identification.

• Resource
• SciCrunch
• 16 years ago - by Anonymous

A non profit organization dedicated to providing support for patients and families with Alzheimer's disease, to educating the public about the disease, to funding a wide range of Alzheimer's disease related research and to finding ways to treat and eventually to prevent Alzheimer's disease. Resources include: the Alzheimer's Association Green-Field Library, a research grants program, and the Journal of the Alzheimer's Association.

• Resource
• SciCrunch
• 16 years ago - by Anonymous

A database of human, chimpanzee, mouse, and rat proteases and protease inhibitors, as well as as the growing number of hereditary diseases caused by mutations in protease genes. Analysis of the human and mouse genomes has allowed us to annotate 581 human, 580 chimpanzee, 667 mouse, and 655 rat protease genes. Proteases are classified in five different classes according to their mechanism of catalysis. Proteases are a diverse and important group of enzymes representing >2% of the human, chimpanzee, mouse and rat genomes. This group of enzymes is implicated in numerous physiological processes. The importance of proteases is illustrated by the existence of 99 different hereditary diseases due to mutations in protease genes. Furthermore, proteases have been implicated in multiple human pathologies, including vascular diseases, rheumatoid arthritis, neurodegenerative processes, and cancer. During the last ten years, our laboratory has identified and characterized more than 60 human protease genes. Due to the importance of proteolytic enzymes in human physiology and pathology, we have recently introduced the concept of Degradome, as the complete repertoire of proteases expressed by a tissue or organism. Thanks to the recent completion of the human, chimpanzee, mouse, and rat genome sequencing projects, we were able to analyze and compare for the first time the complete protease repertoire in those mammalian organisms, as well as the complement of protease inhibitor genes. This webpage also contains the Supplementary Material of Human and mouse proteases: a comparative genomic approach Nat Rev Genet (2003) 4: 544-558, Genome sequence of the brown Norway rat yields insights into mammalian evolution Nature (2004) 428: 493-521, A genomic analysis of rat proteases and protease inhibitors Genome Res. (2004) 14: 609-622, and Comparative genomic analysis of human and chimpanzee proteases Genomics (2005) 86: 638-647.

• Resource
• SciCrunch
• 17 years ago - by Anonymous

Assembly package that contains a suite of software programs for correcting errors in short reads and assembling them. The assembler may take as input classical Sanger reads, 454 sequences, and Illumina reads.

• Resource
• SciCrunch
• 13 years ago - by Anonymous

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 31,2025. A standard next-generation paper (NGP) digital format for reading and digitally archiving scientific research papers to offer better imaging, data sharing and an improved reading experience. The NGP format is designed to retain traditional elements (i.e. Abstract, Introduction, etc.). Papers are viewed using any web browser running on any computing platform, including mobile devices. A button menu system provides navigation between pages. The format provides a more streamlined reading experience by providing as much information to the reader inline as possible, without requiring the user to skip between pages. To accomplish this, pop-up figure and reference details provide additional information without disrupting the flow of the paper. Clicking on standard figure data reveals full-resolution images, and live web links can be optionally followed from pop-up citations or inline links for additional information. Multimedia, such as hi-definition video or audio clips, is easily embedded within the new NGP format. The reader may also customize their reading experience by selecting alternative text and background color themes. The NGP format was created using non-proprietary open-source software including HTML and Javascript, and can be packaged to run offline independent of a live Internet connection. Data are fully captured and communicated utilizing the latest technologies available. The SCORE Imaging (Petzold et al.) paper was submitted to the publisher using this format to take advantage of its superior technical capabilities (http://zfishbook.org/NGP/).

• Resource
• SciCrunch
• 15 years ago - by Anonymous

A database of animal, plant and virus microRNA data maintained at the University of Poznan. The database provides: * 9980 miRNA candiates from 420 animal and plant species predicted in Expressed Sequence Tags * predicted targets for plant candidates * RNA-seq reads mapped to candidates from 29 species * external data from 12 databases that includes sequences, polymorphism, expression and regulation. miRNEST 1.0, it contains miRNA from 563 animals, plants and viruses plant species.

• Resource
• SciCrunch
• 15 years ago - by Anonymous

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on February 28,2023. Software program for visualizing annotations of genomic sequences. The program has features such as the ability to create comprehensive plots, customizable parameters, and flexibility in file format.

• Resource
• SciCrunch
• 17 years ago - by Anonymous

THIS RESOURCE IS NO LONGER IN SERVICE, documented on August 18, 2016. icyou is an internet resource of health-related video clips submitted by users. Health topics covered in videos can range anywhere from infectious diseases to fitness and exercise, with videos generally being shorter than 10 minutes in length. Videos also contain information on treatment and procedures, medical fields, and health politics and policy. These videos may or may not be authored by licensed medical personnel. All videos are searchable, and users can also choose to upload their own healthcare-related videos. In addition to gathering healthcare video from the best sources on the Web and beyond, icyou.com can call on its own award-winning health reporting team to cover the latest issues and trends. Through its parent company Benefitfocus, icyou.com has full access to the Benefitfocus Media Studio, a state-of-the-art HD facility located in Charleston, South Carolina. This studio is the only one of its kind devoted solely to creating healthcare-oriented video content. In it, the Benefitfocus Media team creates up-to-the-minute reports, tutorials, features and more that help illuminate its users about the complexities of the many facets of healthcare.

• Resource
• SciCrunch
• 17 years ago - by Anonymous

Laboratory portal of the University of Sao Paulo Molecular Genetics and Bioinformatic Laboratory.

• Resource
• SciCrunch
• 15 years ago - by Anonymous

A set of programs that map and assemble fixed-length Solexa/SOLiD reads in a fast and accurate way.

• Resource
• SciCrunch
• 13 years ago - by Anonymous

The mission of the National Parkinson Foundation is to improve the quality of care for people with Parkinson's disease through research, education and outreach. NPF funds research through four main programs: the Centers of Excellence Network, which focuses on clinical studies of new therapeutic approaches; the Parkinson's Outcomes Project, a large clinical study of Parkinson's disease; the Grants/Clinical Research Fund, which provides funding to individual researchers; and fellowship awards, which are used to train neurologists in the movement disorder specialty.

• Resource
• SciCrunch
• 17 years ago - by Anonymous

The Department of Pathology at UT Southwestern Medical Center is committed to its missions in diagnostics, research, teaching, and resident and fellowship training. Our facilities include approximately 54,000 square feet of lab and office space. Our Department comprises more than 100 of the most outstanding faculty in the country and more than 50 residents and fellows. We are home to more than a dozen graduate students at any given time. The Department of Pathology offers comprehensive, in-depth training in all of the various pathology disciplines, as well as a complete array of subspecialty fellowship programs. It is our view that a strong academic environment with access to state-of-the-art and newly emerging diagnostic technologies is essential to the preparation of any pathologist for professional life in the 21st century, regardless of the ultimate practice setting. Therefore, basic training in our program is enhanced by extensive exposure to modern molecular diagnostics, advanced flow cytometric analysis, and molecular cytogenetics. The Department provides diagnostic services in a variety of clinical settings that include a large county hospital (Parkland Memorial Hospital), two private University Hospitals (Zale-Lipshy and St. Paul), a tertiary care private pediatric hospital (Children''s Medical Center), a large university outpatient clinic (Aston Clinic), and the Dallas VA Medical Center, exposing our residents, fellows, and faculty to the full spectrum of human adult and pediatric disease.

• Resource
• SciCrunch
• 15 years ago - by Anonymous

An algorithm to align LC-MS samples and to match corresponding ion species across samples.

• Resource
• SciCrunch
• 12 years ago - by Anonymous

Example Slicer3 plugins that can be built against a Slicer3 build or a Slicer3 installation. Note: these are for 3D Slicer version 3. There is now a version 4 of 3D Slicer available. Information about extensions for version 4 can be found at the following links: http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/SlicerApplication/ExtensionsManager http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Developers/Tutorials/BuildTestPackageDistributeExtensions

• Resource
• SciCrunch
• 14 years ago - by Anonymous

The DualSurfaceMin is a C++ implementation of the fully automatic dual surface minimization (DSM) algorithm for the optimization of deformable surfaces. The method is developed for automatic surface extraction from noisy volumetric images. Its features include: global DSM, DSM-OS, and DSM-IS algorithms for automatic surface extraction from volumetric images using deformable simplex meshes; support for the VRML and OFF formats; output pf both triangulated and simplex meshes; and support for the raw and Analyze 7.5 image formats.

• Resource
• SciCrunch
• 17 years ago - by Anonymous

Software Python package that provides support for basic COnstraint-Based Reconstruction and Analysis (COBRA) methods.

• Resource
• SciCrunch
• 12 years ago - by Anonymous