NCBI Comparative Genomics Codeathon: NCBI Resources for Participants

ClinicalTrials.gov

ClinicalTrials.gov is a database of privately and publicly funded clinical studies conducted around the world.

ClinVar

ClinVar aggregates information about genomic variation and its relationship to human health.

dbGaP

The database of Genotypes and Phenotypes (dbGaP) archives and distributes data and results from studies investigating the interaction of genotype and phenotype in humans.

Genetic Testing Registry (GTR)

Genetic Testing Registry (GTR®) provides a central location for voluntary submission of genetic test information by providers. The scope includes the test's purpose, methodology, validity, evidence of the test's usefulness, and laboratory contacts and credentials. The overarching goal of the GTR is to advance the public health and research into the genetic basis of health and disease.

MedGen

MedGen organizes information related to human medical genetics, such as attributes of conditions with a genetic contribution.

Medical Genetics Summaries

A growing collection of summaries which review genetic variants that underlie inherited conditions, affect the risk of developing a disease in the future, or influence how an individual may respond to a specific drug.

   

Variation Resources:  dbSNP & dbVar

Resources for human genomic variations, including both common and rare short and large structural variations.

dbSNP contains human single nucleotide variations, microsatellites, and small-scale insertions and deletions along with publication, population frequency, molecular consequence, and genomic and RefSeq mapping information for both common variations and clinical mutations.

dbVar is a database of human genomic Structural Variation, including large (>50 bp) insertions, deletions, duplications, inversions, mobile elements, translocations, and complex variants.

BLAST

BLAST® finds regions of similarity between biological sequences. The program compares nucleotide or protein sequences to sequence databases and calculates the statistical significance.

Comparative Genome Viewer (CGV)

The Comparative Genome Viewer (CGV) tool allows you to compare two genomes based on assembly-assembly alignments provided by NCBI.

  

Eukaryotic Genome Annotation Pipeline (EGAPx)

EGAPx is the publicly accessible version of the updated NCBI Eukaryotic Genome Annotation Pipeline. The pipeline uses a modular framework for annotation tasks from the fetching of raw and curated data from NCBI's public sequence repositories to the alignment of sequences and the prediction of gene locations.

Foreign Contamination Screen (FCS)

The NCBI Foreign Contamination Screen (FCS) is a tool suite for identifying and removing contaminant sequences in genome assemblies. Contaminants are defined as sequences in a dataset that do not originate from the biological source organism and can arise from a variety of environmental and laboratory sources. FCS will help you remove contaminants from genomes before submission to GenBank.

Genome Data Viewer (GDV)

The Genome Data Viewer (GDV) supports the exploration and analysis of NCBI-annotated and selected non-NCBI annotated eukaryotic genome assemblies. Currently, assemblies from over 1600 organisms are available.

Multiple Comparative Genome Viewer (MCGV)

The Multiple Comparative Genome Viewer (MCGV) is a visualization tool for exploring multiple whole genome eukaryotic alignments.

NCBI Datasets

NCBI Datasets is a new resource that lets you easily gather data from across NCBI databases in the website or with command-line tools or APIs. Find and download gene, transcript, protein and genome sequences, annotation and metadata.

GenBank

GenBank® is the NIH genetic sequence database, an annotated collection of all publicly available DNA sequences. GenBank is part of the International Nucleotide Sequence Database Collaboration, which comprises the DNA DataBank of Japan (DDBJ), the European Nucleotide Archive (ENA), and GenBank at NCBI. These three organizations exchange data on a daily basis.

MANE

The Matched Annotation from the NCBI and EMBL-EBI (MANE) is a collaborative project that aims to converge on human gene and transcript annotation and to define a genome wide set of representative transcripts and corresponding proteins for human protein-coding genes. 

The NCBI Submission Portal

NCBI's Submission Portal allows you to submit your data to the world's largest public repository of biological and scientific information.

PubChem

PubChem is an open chemistry database which has become a key chemical and biochemical information resource for scientists, students, and the general public.

RefSeq

The NCBI Reference Sequence Database (RefSeq) is a comprehensive, integrated, non-redundant, well-annotated set of reference sequences including genomic, transcript, and protein.

Sequence Read Archive (SRA)

Sequence Read Archive data, available through multiple cloud providers and NCBI servers, is the largest publicly available repository of high throughput sequence data. The archive accepts data from all branches of life as well as metagenomic and environmental surveys.

PubMed

PubMed® comprises more than 34 million citations for biomedical literature from MEDLINE, life science journals, and online books. Citations may include links to full text content from PubMed Central and publisher web sites.

PubMed Central (PMC)

PubMed Central® (PMC) is a free full-text archive of biomedical and life sciences journal literature.