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1 Building a new genome database - genomewiki
http://genomewiki.ucsc.edu/index.php/Building_a_new_genome_database
Building a new genome database · 1. Organize your work. · 2. You should have fasta file(s) of your genome sequence and an AGP file describing ...
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2 Building a Custom Reference Genome Database | metacache
https://muellan.github.io/metacache/building.html
Building a database · Step 1: Configure a new genome in SnpEff's config file snpEff.config . · Step 2: Build using gene annotations and reference sequences · Step ...
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3 A Building Block for a Model Organism System Database
https://genome.cshlp.org/content/12/10/1599.full.html
Along with genetic and physical map rendering tools, Web-based genome browsers are a class of application that the bioinformatics research community seems to be ...
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4 BioCyc Pathway/Genome Database Collection
https://biocyc.org/
BioCyc integrates sequenced genomes with predicted metabolic pathways for thousands of organisms, ... Webinar #6: Creating a Pathway/Genome Database.
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5 Free Online Tutorials Teach Anyone How to Use Genome ...
https://www.genome.gov/27530225/free-online-tutorials-teach-anyone-how-to-use-genome-databases
Sequence data from numerous genomic projects are pouring out of the ... Moreover, there is a shortage of bioinformatics experts, making it ...
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6 Genomic Data Resources: Challenges and Promises - Nature
https://www.nature.com/scitable/topicpage/genomic-data-resources-challenges-and-promises-743721/
Along with this rise, the number and types of genomic databases have also ... sequences and build on them to create curated, accurate sequence data.
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7 Genomic Database - an overview | ScienceDirect Topics
https://www.sciencedirect.com/topics/biochemistry-genetics-and-molecular-biology/genomic-database
The earliest genomic databases were created with the intention of making DNA sequences from a variety of living organisms available, without restrictions on the ...
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8 General genomics databases and tools | HSLS
https://www.hsls.pitt.edu/obrc/index.php?page=general_genomics
A web server for you to create your own idiogram. Integr8 and Genome Reviews -- integrated views of complete genomes and proteomes. Explore the biology of ...
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9 Hospital and Drugmaker Move to Build Vast Database of New ...
https://www.nytimes.com/2022/08/12/nyregion/database-new-yorkers-dna.html
(Those two government projects involve whole-genome sequencing, which reveal an individual's complete DNA makeup; the Mount Sinai project will ...
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10 Ensembl genome browser 108
https://www.ensembl.org/index.html
BioMart >. Export custom datasets from Ensembl with this data-mining tool ; BLAST/BLAT >. Search our genomes for your DNA or protein sequence ; Variant Effect ...
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11 Genome build information is an essential part of genomic track ...
https://genomebiology.biomedcentral.com/articles/10.1186/s13059-017-1312-1
In the GEO database, we examined all the records (one sample per series) that involved high-throughput sequencing submitted after 31 December ...
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12 Saccharomyces Genome Database | SGD
https://www.yeastgenome.org/
The Saccharomyces Genome Database (SGD) provides comprehensive integrated biological information for the budding yeast Saccharomyces cerevisiae.
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13 The Cancer Genome Atlas Program - NCI
https://www.cancer.gov/about-nci/organization/ccg/research/structural-genomics/tcga
Access TCGA data through the Genomic Data Commons Data Portal, along with web-based analysis and visualization tools. TCGA Cancers Selected for Study. An ...
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14 Year of the Rat: The Rat Genome Database at 20: a multi ...
https://academic.oup.com/nar/article/48/D1/D731/5622704
In recent years, RGD has developed a suite of tools to easily create and analyze a list of genes. These can be accessed from the 'Analysis & Visualization' link ...
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15 Custom Genomes - Galaxy Community Hub
https://galaxyproject.org/learn/custom-genomes/
Some tools and functions require that the 'database' attribute is assigned or that a Custom Reference Genome is set up as a Custom Build prior to use. Examples ...
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16 Illumina | Sequencing and array-based solutions for genetic ...
https://www.illumina.com/
Illumina sequencing and array technologies fuel advancements in life science research, translational and consumer genomics, and molecular diagnostics.
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17 Genomics | Broad Institute
https://www.broadinstitute.org/genomics
Since the Human Genome Project in the 1990s, the Broad Genomics Platform has ... Our goal has been two-fold: to create foundational genomics resources and ...
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18 International Tomato Genome Sequencing Project
https://solgenomics.net/organism/Solanum_lycopersicum/genome
The genome data is available from our FTP site (Build SL4.0 and ITAG4.0), ... The initial approach was to sequence only the euchromatic sequence using a ...
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19 Rat Genome Database
https://rgd.mcw.edu/
The Rat Genome Database houses genomic, genetic, functional, physiological, pathway and disease data for the laboratory rat as well as comparative data for ...
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20 China's gene giant harvests data from millions of pregnant ...
https://www.reuters.com/investigates/special-report/health-china-bgi-dna/
DNA data collected from prenatal tests on women outside China has also been stored in China's government-funded gene database, one of the ...
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21 Genomics on AWS | Healthcare & Life Sciences
https://aws.amazon.com/health/genomics/
Sequence Bio gains agility for large-scale genomic analysis on AWS. Read the case study ». Build machine learning models on genomic datasets using AWS.
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22 How do I build a genome database of closely-related taxa to ...
https://www.researchgate.net/post/How-do-I-build-a-genome-database-of-closely-related-taxa-to-my-organism
Once you have the genomes you want, you can build your database with the BLAST commands, and then perform your analysis. Cite.
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23 The complete sequence of a human genome | Science
https://www.science.org/doi/10.1126/science.abj6987
ONT reads spanning two or more rDNA units were used to build a morph graph representing the structure of each array (fig. S12). The shorter ...
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24 gmap_build - Tool for genome database creation for GMAP or ...
https://manpages.ubuntu.com/manpages/bionic/man1/gmap_build.1.html
gmap_build: Builds a gmap database for a genome to be used by GMAP or GSNAP. Part of GMAP package, version 2017-11-15. A simplified alternative to using the ...
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25 Genomic Databases - Finding Datasets for Secondary Analysis
https://browse.welch.jhmi.edu/datasets/genomic-databases
The 1000 Genomes Project ran between 2008 and 2015, creating the largest public catalogue of human variation and genotype data. As the project ...
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26 How are sequenced genomes stored and shared?
https://www.yourgenome.org/facts/how-are-sequenced-genomes-stored-and-shared/
Once a genome? sequence has been assembled and annotated the information needs to be stored in a database so that it can be shared with lots ...
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27 DECIPHER v11.16: Mapping the clinical genome
https://www.deciphergenomics.org/
The DECIPHER database contains data from 45,330 patients who have given consent for ... It's still free, and you are in control of what data to make public.
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28 Automated Querying of Genome Databases - PLOS
https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.0030001
Genome databases offer solutions to this problem by integrating data from multiple databases in a uniform and standardized manner. However, ...
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29 MGI-Mouse Genes, Genome Features & Maps
http://www.informatics.jax.org/genes.shtml
Genes and Markers Query; Create a display of regions of the mouse genome. ... Input a list of gene IDs or symbols and retrieve other database IDs and gene ...
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30 Genetics & Genomics - WSU Tree Fruit
http://treefruit.wsu.edu/varieties-breeding/genetics-genomics/
Building on the Genome Database for Rosaceae (GDR), tree fruit Genome ... genomics-assisted-breeding, and enhance critical decision-making by apple, cherry, ...
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31 Building a Genome Database Using an Object-Oriented ...
https://content.iospress.com/articles/in-silico-biology/isb00043
The most important data in GOBASE, i. e., molecular sequences and taxonomic information, are obtained from the public sequence data repository ...
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32 What are whole exome sequencing and whole genome ...
https://medlineplus.gov/genetics/understanding/testing/sequencing/
The Sanger method has been automated to make it faster and is still used in laboratories today to sequence short pieces of DNA, ...
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33 Geneious | Bioinformatics Software for Sequence Data Analysis
https://www.geneious.com/
Geneious Prime is the world's leading bioinformatics software platform for molecular biology and sequence analysis. Enterprises involved in antibody ...
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34 The Bovine Genome Database | BovineGenome.org
https://bovinegenome.elsiklab.missouri.edu/
The goal of BovineMine is to accelerate genomics analysis by enabling researchers without scripting skills to create and export customized annotation datasets ...
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35 TGD | Tetrahymena Genome Database Wiki
https://www.ciliate.org/
and/or through independent research projects. The workshop will cover how to weigh various forms of evidence to make predictions of gene structure using the ...
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36 Expasy: SIB Swiss Institute of Bioinformatics
https://www.expasy.org/
SIB Resources · Evolution biology. Software tool. Nextstrain · Genes & Genomes; , Genomics; , Transcriptomics · Proteins & Proteomes. Database. UniProtKB/Swiss- ...
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37 GeneCards - Human Genes | Gene Database | Gene Search
https://www.genecards.org/
GeneCards is a searchable, integrated, database of human genes that provides concise genomic related information, on all known and predicted human genes.
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38 Candidate Cancer Gene Database
http://ccgd-starrlab.oit.umn.edu/
The idea for creating this database originated from Tim Starr, Vincent Keng, and David Largaespada at UMN. Erik Nyre and Ken Abbott developed the original ...
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39 Mouse Genomes Project - Wellcome Sanger Institute
https://www.sanger.ac.uk/data/mouse-genomes-project/
About · Short-read sequencing of many laboratory mouse strains and identification of sequence variation (SNPs, short insertions and deletions, and larger ...
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40 How to build genome database - chip-seq-pipeline2 - GitHub
https://github.com/ENCODE-DCC/chip-seq-pipeline2/blob/master/docs/build_genome_database.md
How to build genome database · Install Conda. · Install pipeline's Conda environment. · Choose GENOME from hg19 , hg38 , mm9 and mm10 and specify a destination ...
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41 Welcome to ClinGen
https://clinicalgenome.org/
... of Health (NIH)-funded resource dedicated to building a central resource that ... ClinGen was founded in 2013 by the National Human Genome Research ...
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42 MetaCyc: Metabolic Pathways From all Domains of Life
https://metacyc.org/
MetaCyc Metabolic Pathway Database · Online encyclopedia of metabolism · Predict metabolic pathways in sequenced genomes · Support metabolic engineering via enzyme ...
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43 Kraken - CCB at JHU - Johns Hopkins University
https://ccb.jhu.edu/software/kraken/
These can largely be eliminated by first running the 'dust' program on all genomes and then building the database from these 'dusted' genomes.
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44 readme - GenomeNet
https://www.genome.jp/ftp/tools/dbget/README
DBGET is an integrated database retrieval system for the following biological databases. For more details, see https://www.genome.jp/dbget/.
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45 1000 Genomes | A Deep Catalog of Human Genetic Variation
http://www.internationalgenome.org/
The International Genome Sample Resource ... The 1000 Genomes Project created a catalogue of common human genetic variation, using openly consented samples from ...
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46 Mayo Clinic to sequence 100K participants to build genomic ...
https://newsnetwork.mayoclinic.org/discussion/mayo-clinic-to-sequence-100k-participants-to-build-genomic-database-for-improved-care-and-research-in-collaboration-with-helix/
Mayo Clinic to sequence 100K participants to build genomic database for improved care and research in collaboration with Helix.
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47 Bioinformatics Databases - Subject Guides
https://subjectguides.lib.neu.edu/c.php?g=948457&p=6839134
A searchable database of genes, focusing on genomes that have been completely sequenced and that have an active research community to contribute gene-specific ...
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48 Catalogue of Genomic Data Initiatives - GA4GH
https://www.ga4gh.org/community/catalogue/
Initiative type: Database. The 1000 Genomes Project set out to catalogue common human genetic variation, publishing a set of variations based on sequencing ...
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49 whole genome sequencing (WGS) - CDC
https://www.cdc.gov/pulsenet/pathogens/wgs.html
The sequencer identifies the A's, C's, T's, and G's, or bases, that make up each bacterial sequence. The sequencer uses the bar code to keep track of which ...
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50 Build a Custom Reference (cellranger mkref) -Software - Support
https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/using/tutorial_mr
First, locate the reference genome FASTA and GTF files for your species. If the species is available from the Ensembl database, we recommend using the files ...
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51 Toward a genome sequence for every animal - PNAS
https://www.pnas.org/doi/10.1073/pnas.2109019118
The first animal genome sequence was published 23 y ago (1). ... To construct a database of the best available genome assembly for all animals, ...
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52 The Human Gene Mutation Database - Springer Link
https://link.springer.com/article/10.1007/s00439-013-1358-4
The Human Gene Mutation Database: building a comprehensive mutation repository for clinical and molecular genetics, diagnostic testing and ...
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53 Indigenous Genomic Databases: Pragmatic Considerations ...
https://www.frontiersin.org/articles/10.3389/fpubh.2020.00111/full
The potential to grow genomic knowledge and harness the subsequent clinical benefits has escalated the building of background variant databases (BVDs) for ...
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54 CLC Microbial Genomics Module latest improvements
https://digitalinsights.qiagen.com/clc-microbial-genomics-module-latest-improvements/
Create Annotated Sequence List is a general sequence annotation tool that can be used to set up many different databases (annotated sequence lists) used in the ...
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55 Understanding the Global Landscape of Genomic Initiatives
https://www.iqvia.com/insights/the-iqvia-institute/reports/understanding-the-global-landscape-of-genomic-initiatives
This report utilizes the IQVIA Genomic Initiatives Database and ... opening new opportunities to build repositories of genomic data.
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56 Configuring, Updating, and Customizing HOMER
http://homer.ucsd.edu/homer/introduction/update.html
In an effort to make sure things are standardized for analysis, HOMER organizes promoters, genome sequences and annotation into packages.
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57 For the first time, India has a genome database. But are we ...
https://theprint.in/opinion/india-has-genome-database-for-first-time-are-we-ready-to-use-it/324346/
The IndiGen Genome Project, launched in April this year, is a government-funded exercise that sequenced more than a thousand individuals ...
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58 First studies from largest-ever human genome database ...
https://www.sciencefocus.com/the-human-body/first-studies-from-largest-ever-human-genome-database-released/
What became clear was that we desperately needed better databases of normal variation [in genomes] to make sense of the genetic changes that we ...
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59 Mascot database search: Sequence database setup: Generic ...
https://www.matrixscience.com/help/seq_db_setup_generic.html
For a protein Fasta file downloaded from NCBI, create a new custom ... There are many routes to get to the genome sequence data and there is a choice of ...
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60 Building a sequence map of the pig pan-genome from multiple ...
https://www.biorxiv.org/content/10.1101/459453v2.full
PIGPAN is a comprehensive repository of integrated genomics, transcriptomics and regulatory data. The system diagram is shown in Fig. 5a. In our ...
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61 The impact of genomics on the future of medicine and health
https://www.mja.com.au/journal/2014/201/1/impact-genomics-future-medicine-and-health
Making sense of genomic data requires computational technologies and databases to evolve in parallel with sequencing technologies.
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62 GenomeSpace Tools and Data Sources
https://genomespace.org/support/tools/
The ArrayExpress Archive is a database of functional genomics data; ... large panel of human cancer models and to develop integrated computational analyses ...
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63 SequenceServer: Custom BLAST analysis server for you and ...
https://sequenceserver.com/
Rapidly set up a BLAST+ server for yourself or for sharing datasets with your ... Triant (2020) Using online tools at the Bovine Genome Database to manually ...
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64 Pig Genome Database
https://www.animalgenome.org/pig/genome/db/
The Pig Genome Database (PGD) is to serve the purpose not only to bring together pig ... Click on a chromosome to get a quick GBrowse view on Build 10.2:.
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65 Toward a Shared Vision for Cancer Genomic Data | NEJM
https://www.nejm.org/doi/full/10.1056/nejmp1607591
Often, genomic studies are published without the authors' providing raw sequencing data in a public repository, making it impossible to judge ...
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66 Genomic data processing reference architecture - Google Cloud
https://cloud.google.com/architecture/genomic-data-processing-reference-architecture
After creating mapped DNA reads from samples, you transfer these BAM files to a Cloud Storage bucket. · You authenticate to act as a service ...
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67 Tutorial — inStrain 1.0.0 documentation
https://instrain.readthedocs.io/en/master/tutorial.html
Tutorial #3 describes how to combine custom genomes with an existing genome database. This allows users to include both sample-specific ...
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68 Regeneron Genetics Center (RGC): Human DNA Sequencing
https://www.regeneron.com/science/genetics-center
Regeneron Genetics Center ONE OF THE WORLD'S LARGEST HUMAN GENOMIC ... exome sequence data from the 500,000 volunteer participants who make up the UK ...
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69 Lotus japonicus genome assembly build 3.0
https://www.kazusa.or.jp/lotus/
Kazusa DNA Research Institute is pleased to release Lotus japonicus genome assembly build 3.0. Summary of build 3.0 · Database of build 2.5 (previous ...
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70 BSubCyc | Encyclopedia of Bacillus Subtilis Subtilis Genes ...
https://bsubcyc.org/
BsubCyc is a model-organism database for the bacterium Bacillus subtilis and is based on the updated B. subtilis 168 genome sequence and annotation ...
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71 GWAS Catalog - EMBL-EBI
https://www.ebi.ac.uk/gwas/
The NHGRI-EBI GWAS Catalog: a curated collection of all human genome-wide association studies, produced by a collaboration between EMBL-EBI and NHGRI.
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72 Reference genome - Wikipedia
https://en.wikipedia.org/wiki/Reference_genome
A reference genome is a digital nucleic acid sequence database, assembled by scientists as a representative example of the set of genes in one idealized ...
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73 Global Genome Initiative (GGI)
http://naturalhistory.si.edu/research/global-genome-initiative
The Global Genome Biodiversity Network will serve to accelerate and optimize research everywhere. Its goal is to achieve one federated database of the world's ...
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74 Accelerating genomics workflows and data analysis on Azure
https://azure.microsoft.com/en-us/blog/accelerating-genomics-workflows-and-data-analysis-on-azure/
The research teams are starting to sequence fish genomes in the hundreds and were looking for Azure based solutions for scaling and ...
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75 International Sheep Genomics Consortium
https://www.sheephapmap.org/
The Sheep Genomes Database has the following three key objectives: collect and make available sheep genome data on behalf of the community; provide variant ...
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76 GenAge: The Ageing Gene Database
https://genomics.senescence.info/genes/index.html
Welcome to GenAge, the benchmark database of genes related to ageing. GenAge is divided into ... Release notes for the current build are also available.
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77 Google Is Giving Away AI That Can Build Your Genome ...
https://www.wired.com/story/google-is-giving-away-ai-that-can-build-your-genome-sequence/
Google Is Giving Away AI That Can Build Your Genome Sequence. The deep learning tool can identify all the small mutations that make you ...
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78 Genetic data - UK Biobank
https://www.ukbiobank.ac.uk/enable-your-research/about-our-data/genetic-data
Whole-exome sequencing measures the regions of the genome (about 2%) that are involved in coding for proteins and is particularly suitable for ...
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79 Create bowtie2 index - Metagenomics
https://www.metagenomics.wiki/tools/bowtie2/index
How to create a bowtie2 index database of multiple genomes? · # Merge all E. · # create bowtie2 index database · # result: 6 . · # use 'inspect' to check the ...
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80 Which Reference Genome and Strand Does 23andMe Use?
https://customercare.23andme.com/hc/en-us/articles/212883767-Which-Reference-Genome-and-Strand-Does-23andMe-Use-
Consult with a healthcare professional before making any major lifestyle changes. ... example of the nucleotide sequence of the genome for a species.
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81 Tutorial 7: Constructing new databases using ARB
https://hahana.soest.hawaii.edu/cmoreserver/education/grads-postdocs/arb_downloads/Tutorial_7_new%20database.doc
Tutorial 7: Creating and working with new databases ... ARB is most frequently utilized for management and analysis of SSU rRNA gene data, but it can be a ...
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82 DNA databases - ISOGG Wiki
https://isogg.org/wiki/DNA_databases
Human mitochondrial genome database For a description see: Ingman M, Gyllensten U. ... DNA to create a YDNA and mitochondrial DNA database.
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83 FlyBase Homepage
https://flybase.org/
FlyBase: a database for drosophila genetics and molecular biology. ... Human Disease; Protein Domains; Gene Groups; Pathways; GO; Data Class
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84 TeaPGDB: Tea Plant Genome Database
https://www.maxapress.com/article/doi/10.48130/BPR-2021-0005
The current release of TeaPGDB hosts published tea plant genome data ... this database not only contains more complete genome data and gene ...
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85 The Rise of the Private Genome Databases | by StartUp Health
https://healthtransformer.co/the-rise-of-the-private-genome-databases-42a14d5988f5
“WuXi NextCode is joining a global movement that's aimed at collecting enough genomic data to make breakthroughs in cancer and longevity.”.
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86 GenomeTrakr Network - FDA
https://www.fda.gov/food/whole-genome-sequencing-wgs-program/genometrakr-network
FDA encourages those labs to sequence those isolates and upload the genomic information to the GenomeTrakr database at NCBI.
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87 Human Genome Editing (HGE) Registry
https://www.who.int/groups/expert-advisory-committee-on-developing-global-standards-for-governance-and-oversight-of-human-genome-editing/registry
The Human Genome Editing (HGE) Registry is a central database that collects ... HGE Registry aims at making information about clinical trials using genome ...
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88 UniProt
https://www.uniprot.org/
UniProt is the world's leading high-quality, comprehensive and freely accessible resource of protein sequence and functional information.
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89 Nebula Genomics - 30x Whole Genome Sequencing - DNA ...
https://nebula.org/whole-genome-sequencing-dna-test/
You get access to the world's largest Y-DNA and mtDNA databases where you can trace your parents' lines, find relatives, and build your family tree. Genome ...
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90 Efficient storage and analysis of genome data in relational ...
https://d-nb.info/1136955135/34
use relational database technology in the context of genome analysis mainly ... make database-integrated variant detection a competitive ...
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91 Genomics England: Homepage
https://www.genomicsengland.co.uk/
Enabling scientific research via our large genomic database. Our secure Research Environment equips approved researchers to make discoveries that enhance ...
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92 GISAID - gisaid.org
https://gisaid.org/
hCoV-19 data sharing via GISAID. 14,095,158. genome sequence submissions. GISAID Resources. Data Acknowledgement Locator. Example ID ...
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93 China's BGI says it can sequence a genome for just $100
https://www.technologyreview.com/2020/02/26/905658/china-bgi-100-dollar-genome/
Using technology originally acquired in the US, the Chinese gene giant BGI Group says it will make genome sequencing cheaper than ever, ...
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94 Plant Genome Database Tutorial - USDA
https://wheat.pw.usda.gov/ggpages/links/tutorial/Default.htm
The Plant Genome Databases - A Tutorial · Lesson 1 - Overview of Demeter's Genomes Home Page · Lesson 2 - Overview of Genetic Maps · Lesson 3 - Creating the Map ...
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95 Public Data and Reproducible Bioinformatics – - Meren Lab
https://merenlab.org/data/
We deposited the long-read sequencing data in the NCBI's SRA database for ... A reproducible workflow to detail the steps of genome refinement and make ...
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