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iPOP / integrated Personal Omics Profiling
Gives a multi-dimensional view of medical states. iPOP includes healthy states, response to viral infection, recovery, and Type 2 Diabetes (T2D) onset. The database aims to (1) determine the genome sequence at high accuracy and evaluate disease risks, (2) survey omics components over time and integrate the relevant omics information to assess the variation of physiological states, and (3) investigate the expression of personal variants at the level of RNA protein.
Contains traits on clonal growth and vegetative regeneration for the European temperate flora. CLO-PLA is a database that can help to assess the roles of vegetative means of regeneration and spread in plant communities under the effect of various biotic and abiotic filters. It can serve as a source of reference on persistence traits of European temperate flora and, eventually, as a guide for trait sampling in other regions of the world. CLO-PLA provides basic and detailed information referring to the most widely applied terms required for studying vegetative organs. This offers an easy self-education opportunity for researchers willing to improve their expertise in this field.
DAGViz / Directed Acyclic Graphs Viewer
Allows users to perform functional analyses using Gene Ontology (GO) annotations in various organisms. DAGViz is a Directed Acyclic Graphs (DAG)-based browser that facilitates the integrative analysis of functional categories associated with a gene product by displaying all DAG-based information for multiple GO terms using a tabulated color chart screen. This resource provides GO annotation datasets for 45 organisms including fungi, protist, animal, plant and bacterial species.
ARGs-OSP / Antibiotic Resistant Genes Online Searching Platform
Provides an online searching platform for antibiotic resistant genes (ARGs). ARGs-OSP is a database that offers a global profile of the antibiotic resistome. This resource was constructed by integrating two large datasets of the whole genome database (WGD) and metagenomic database (MGD). It includes search and download functionalities that were designed for users to retrieve the occurrence of ARGs in different taxonomy and the abundance of ARGs in different habitats.
Provides a resource for the development and validation of exome-based clinical panels. ExomeSlicer is a web-based tool for the identification of gene-specific and exome-wide technically challenging regions that cannot be reliably sequenced. It can be a source of false positive and/or false negative variant calls. This method supports exome-based and targeted panel development through identification of potential ancillary testing, characterization of test limitation, and streamlining post hoc Sanger sequencing.
Consists of a novel neural network implementation applying ribosome profiling data for the annotation of translation start site (TISs) in prokaryotes. DeepRibo applies both convolutional neural network (CNN) and recurrent neural network (RNN) architectures for attaining and combining information from the ribosome profiling signal and DNA sequence. It is trained on a combination of available experiments for different bacteria and has been tested on de novo ribo-seq data of bacterial genomes.
Gathers annotation and analysis of binding sites for site-specific transcription factors in the promoter and enhancer regions of genes. NFI-Regulome provides the control regions of genes that have been shown to be regulated by Nuclear Factor I (NFI) transcription factors in the primary literature. It enables rapid comparisons of the size, composition, and organizational structure of the cis-regulatory regions of NFI-regulated genes, selected either by disease-relevance, cell, tissue or developmental stage.
CHESS / Comprehensive Human Expressed SequenceS
Gathers more than 43000 human genes about 320000 transcripts. CHESS is a repository which proposes five downloadable files displaying: (i) a set for gene annotation aligned according human genome release GRCh38.p8; (ii) a gene list of the complete database with additional features; (iii) a FASTA file including the sequences of the censused proteins; (iv) a modified annotation file limited to reference chromosomes and mitochondrion; and (v) a set of annotation enriched by data from RefSeq.
ZETRAP / Zebrafish Enhancer TRAP transgenic line database
A web-based system that provides data and information to the scientific community about the developmental, genetic and genomic aspects of transgenic zebrafish lines obtained using Tol2 transposon-mediated transgenesis. ZETRAP was expanded further by generation of transgenics expressing the membrane-tethered version of a novel red protein KillerRed. The new version contains the sequence of regions flanking the insertion sites, links to genes in zebrafish genome, and confocal images of embryos/larvae of these transgenics.
Allows organization of data from individual databases into one query-optimized system, using a data warehousing technique specifically designed for descriptive data. EnsMart is based on the principle of creating a generic system from specific data sources, where disparate data can be integrated and interrogated in a flexible, unified, and domain-independent manner. The database provides scalability for large amounts of data, support for integration with third-party data and/or programs, and user interfaces. The solution can be adapted to any database containing descriptive data.
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