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Eutherian comparative genomic analysis protocol as one framework of eutherian gene data set revisions. Protocol integrated gene annotations, phylogenetic analysis and protein molecular evolution analysis with 3 new tests including test of reliability of public eutherian genomic sequences using genomic sequence redundancies, test of contiguity of public eutherian genomic sequences using multiple pairwise genomic sequence alignments and test of protein molecular evolution using relative synonymous codon usage statistics. Public eutherian reference genomic sequence data sets.

• RRID-Legacy
• 11 years ago - submitted by Marko Premzl

Software object for calculation of multiple sequence alignment from set of unaligned sequences or alignments using the TCoffee program.

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• SciCrunch
• 3 years ago - submitted by Edyta Vieth

Software packqge for importation, normalization, visualization, and quality control functions to correct identified sources of variability in array-CGH (Comparative genomic hybridization) experiments.

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• SciCrunch
• 13 years ago - by Anonymous

Ontology that describes the different types of associations between a gene and a disease. It was developed to integrate information from different databases that contain gene-disease associations such as UniProt, CTD, Orphanet, the GWAS Catalog, GAD, MGD, RGD, and LHGDN.

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• SciCrunch
• 15 years ago - by Anonymous

Software core library and API of the Medical Image NetCDF toolkit.

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• SciCrunch
• 3 years ago - submitted by Edyta Vieth

Software R package for Gaussian Process Ranking and Estimation of Gene Expression time-series. The software fits two Gaussian processes (GPs) with an radial basis function (RBF) (+ noise diagonal) kernel on each profile. One GP kernel is initialized wih a short lengthscale hyperparameter, signal variance as the observed variance and a zero noise variance. It is optimized via scaled conjugate gradients (netlab). A second GP has fixed hyperparameters: zero inverse-width, zero signal variance and noise variance as the observed variance. The log-ratio of marginal likelihoods of the two hypotheses acts as a score of differential expression for the profile. Comparison via receiver operating characteristic curves (ROC curves) is performed against Bayesian hierarchical model for the analysis of time-series (BATS) (Angelini et.al, 2007).

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• SciCrunch
• 13 years ago - by Anonymous

A software which enables copy number variation (CNV) detections without using a reference genome. Magnolya directly compares the two next-generation sequences datasets.

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• SciCrunch
• 13 years ago - by Anonymous

Targeted assembly software. It takes as input any number of NGS raw read sets and starter set of input sequences.May be used to Validate assembled sequence, Check if known enzyme is present in metagenomic NGS read set, Enrich unmappable reads by extending them, Check what happens at the extremities of a contig, Check the presence / absence and quantify RNA seq splicing events, Check presence/absence of SNPs or structural variants.

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• SciCrunch
• 3 years ago - submitted by Edyta Vieth

An easy to use software tool for dual color microarray data. Its GUI-Tk based environment lets any non-experienced user perform a basic, but not simple, data analysis just following a wizard. In addition it provides some tools for the developer.

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• SciCrunch
• 13 years ago - by Anonymous

A google drive interface for scientific big data. CyVerse cyberinfrastructure is applicable to all life sciences disciplines and works equally well on data from plants, animals, or microbes. It provides life scientists with computational infrastructure to handle large datasets and complex analyses. Its extensible platforms provide data storage, bioinformatics tools, image analyses, cloud services, and APIs.

• SciCrunch
• 11 years ago - submitted by Anita Bandrowski

Software tool for the design of multiplex pyrosequencing assays.

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• SciCrunch
• 3 years ago - submitted by Edyta Vieth

It's strategy involves Whole Genome Shotgun (WGS) sequencing, in which sequence from the entire genome is generated and reassembled. This method is standard for microbial genome sequencing, and has been successfully applied to Drosophila. Neurospora is an ideal candidate for this approach because of the low repeat content of the genome. Neurospora crassa Database has expanded the scope of its database by including a mitochondrial annotation, incorporating information from the Neurospora compendium, and assigning NCU numbers to tRNA and rRNAs. They have improved the annotation process to predict untranslated regions and to reduce the number of spurious predictions. As a result, version 3 contains 9,826 genes, 794 fewer than version 2. During the initial phase of a WGS project they sequence both ends of the 4 kb inserts from a plasmid library prepared using randomly sheared and sized-selected DNA. The shotgun reads are assembled by recognizing overlapping regions of sequence and making use of the knowledge of the orientation and distance of the paired reads from each plasmid. Obtaining deep sequence coverage though high levels of sequence redundancy assures that the majority of the genome is represented in the initial assembly and that the consensus sequence is of high quality. Their approach toward the initial assembly was conservative, meaning they would rather fail to join sequence contigs that might overlap each other than risk making false joins between two closely related but non-overlapping genomic regions. Hence, the initial assembly contains many sequence contigs and over time these contigs will increase in size and decrease in number as they are joined together. After shotgun sequencing and assembly there was a second phase of sequencing in which additional sequence was obtained from specific regions that were missing from the original assembly or are recognized to be of low quality in the consensus. The Neurospora crassa sequencing project reflects a close collaboration between the Broad Institute and the Neurospora research community. Principal investigators include Bruce Birren and Chad Nusbaum from the Broad Institute, Matt Sachs at the Oregon Graduate Institute of Science and Technology, Chuck Staben at the University of Kentucky and Jak Kinsey at the Fungal Genetics Stock Center at the University of Kansas Medical Center. In addition, we have a larger Advisory Board made up of a number of Neurospora researchers. Sponsors: They have been funded by the National Science Foundation to sequence the N. crassa genome and make the information publicly available.

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• SciCrunch
• 17 years ago - by Anonymous

Formerly a topical portal studying the brain which collected and imaged 1000 human brains, the Brain Observatory has partnered with the Institute for Brain and Society to build virtual laboratories that will feed directly into the database of images and knowledge created in the context of the Human Brain Library. The Brain Observatory will also host exhibits, conferences, and events aimed at promoting a heightened awareness of brain research and how its results can benefit personal brain fitness and mental health.

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• SciCrunch
• 16 years ago - by Anonymous

Software tool for automated structrual variation detection from long-read sequencing using state-of-the-art tools. NextSV3 uses Minimap2 to do read mapping and uses two state-of-the-art SV callers (Sniffles and cuteSV) to do SV calling.

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• SciCrunch
• 3 years ago - submitted by Edyta Vieth

Consortium serving the diabetic complications community that sponsors annual meetings in complications-relevant scientific areas, solicits and funds pilot projects in high impact areas of complications research, and provides resources and data including animal models, protocols and methods, validation criteria, reagents and resources, histology, publications and bioinformatics for researchers conducting diabetic complications research.

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• SciCrunch
• 14 years ago - by Anonymous

A SEED-quality automated service that annotates complete or nearly complete bacterial and archaeal genomes across the entire phylogenetic tree. RAST can also be used to analyze draft genomes.

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• SciCrunch
• 11 years ago - submitted by Kristen Jensen

Software wrapper to speed up downloading process by dividing the work into multiple threads.

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• SciCrunch
• 3 years ago - submitted by Edyta Vieth

Questionnaire developed by physicians in NIDDK's Chronic Prostatitis Collaborative Research Network that can help physicians to accurately measure the severity of prostatitis symptoms and their impact on a patient's lifestyle. The CPSI questionnaire assesses pain, urination, and the effect of chronic prostatitis on daily activities. With this information, researchers and physicians can reliably evaluate whether potential treatments are working. The questionnaire was originally published in the Journal of Urology in August 1999 (Vol. 162, pages 369-375). It is available as a PDF document in English, Spanish, German and Korean.

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• dkNET
• 14 years ago - by Anonymous

Web-based software used for the selection of best-fit models of protein evolution., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

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• RRID-Legacy
• 10 years ago - by Anonymous

Software mapping based, assembly assisted plasmid identification tool that analyzes and gives graphic solution for plasmid identification. Computational pipeline implemented in BASH that maps Illumina reads over plasmid database sequences.

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• SciCrunch
• 3 years ago - submitted by Edyta Vieth