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National Center for Biotechnology Information (NCBI) Set

Resources, databases and tools maintained by The National Center for Biotechnology Information
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Found 18 links

Displaying 15 links

BioSystemsDatabase Content

http://www.ncbi.nlm.nih.gov/biosystems

Protein > Databases

The NCBI BioSystems database centralizes and cross-links existing biological systems databases, increasing their utility and target audience by integrating their pathways and systems into NCBI resources. This integration allows users of NCBI's Entrez databases to quickly categorize proteins, genes and small molecules by metabolic pathway, disease state or other BioSystem type.

NAR Database Issue 2010
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tagsanimals cell membrane computational biology genes genetic databases genomics humans national library of medicine (u.s.) nucleic acid databases protein databases systems biology united states
setsNational Center for Biotechnology Information (NCBI)

BLASTTool Content

http://www.ncbi.nlm.nih.gov/BLAST/

DNA > Gene Prediction
DNA > Sequence Retrieval and Submission
Protein > Sequence Retrieval
RNA > Sequence Retrieval
Sequence Comparison > Similarity Searching

Basic Local Alignment Search Tool (BLAST) finds regions of local similarity between sequences. The program compares nucleotide or protein sequences to sequence databases and calculates the statistical significance of matches. BLAST can be used to infer functional and evolutionary relationships between sequences as well as help identify members of gene families.

NAR Web Server Issue 2004NAR Web Server Issue 2006NAR Web Server Issue 2008
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tagsalgorithms amino acid sequence base sequence factual databases genetic databases genome humans mutation national library of medicine (u.s.) nucleic acid databases nucleic acid sequence homology nucleotides protein databases protein sequence analysis sensitivity and specificity sequence alignment sequence analysis systems integration united states
setsNational Center for Biotechnology Information (NCBI)

dbSNPDatabase Content

http://www.ncbi.nlm.nih.gov/SNP/

DNA > Sequence Polymorphisms
Human Genome > Sequence Polymorphisms

Repository for both single base nucleotide subsitutions and short deletion and insertion polymorphisms; NCBI collaboration with NHGRI.

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tagsgenetic databases human genome humans single nucleotide polymorphism
setsNational Center for Biotechnology Information (NCBI)

Entrez GeneDatabase Content

http://www.ncbi.nlm.nih.gov/gene

DNA > Databases

Entrez Gene is NCBI's database for gene-specific information. Entrez Gene maintains records from genomes which have been completely sequenced, which have an active research community to submit gene-specific information, or which are scheduled for intense sequence analysis.

NAR Database Issue 2011
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tagsgenes genetic databases genomics national library of medicine (u.s.) united states
setsNational Center for Biotechnology Information (NCBI)

Genotyping - NCBITool Content

http://www.ncbi.nih.gov/projects/genotyping/formpage.cgi

Model Organisms > Other Organisms
Sequence Comparison > Other Alignment Tools

The Genotyping tool at the NCBI identifies the genotype (or subtype) of viral sequences by using a sliding window approach to BLAST analysis against reference sequences for different viral subtypes. Results are shown as a graphical output plotting the top-scoring genotype. An alignment tool is also available.

NAR Web Server Issue 2004
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tagsalgorithms dna sequence analysis genetic recombination genotype hepacivirus hepatitis b virus hiv-1 molecular sequence data sequence alignment viral dna viral genes viral genome viruses
setsNational Center for Biotechnology Information (NCBI)

NCBI Assembly ArchiveTool Content

http://www.ncbi.nlm.nih.gov/projects/assembly/

Model Organisms > General Resources

The NCBI Assembly Archive links publically available assembly information with the NCBI Trace Archive\'s raw sequence data.

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tagsbiomedical research bioterrorism genetic databases genome information dissemination national institutes of health (u.s.) national library of medicine (u.s.) research support as topic single nucleotide polymorphism united states
setsNational Center for Biotechnology Information (NCBI)

NCBI BookshelfDatabase Content

http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=Books

Education > General
Literature > Goldmines

Searchable collection of biomedical books linked to terms in PubMed abstracts; when viewing an abstract, click on Books link to see phrases in abstract hyperlinked to book sections.

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NCBI C++ toolkitTool Content

http://www.ncbi.nlm.nih.gov/books/bv.fcgi?call=bv.View..ShowTOC&rid=toolkit.TOC&...

Computer Related > Bio-* Programming Tools
Computer Related > C/C++

The NCBI C++ Toolkit is a collection of C++ modules developed by the NCBI for writing bioinformatics software and applications.

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NCBI Clone RegistryDatabase Content

http://www.ncbi.nlm.nih.gov/genome/clone/

DNA > Mapping and Assembly

A database that integrates information about genomic clones and libraries, including sequence data, genomic position, and distributor information.

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NCBI EpigenomicsDatabase Content

http://www.ncbi.nlm.nih.gov/epigenomics

DNA > Databases

The Epigenomics database is a resource for whole-genome epigenetic data sets. Raw data is processed and mapped to genomic coordinates to generate 'tracks' that are a visual representation of the data. These data tracks can be viewed using popular genome browsers or downloaded for local analysis. The Epigenomics resource also provides the user with a unique interface that allows for intuitive browsing and searching of data sets based on biological attributes.

NAR Database Issue 2011
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tagschromatin epigenomics genetic databases humans
setsNational Center for Biotechnology Information (NCBI)

NCBI GEODatabase Content

http://www.ncbi.nlm.nih.gov/geo/

Expression > Databases

The Gene Expression Omnibus (GEO) database stores over 20,000 microarray- and sequence-based functional genomics studies, and continues to handle the majority of direct high-throughput data submissions from the research community. Multiple mechanisms are provided to help users effectively search, browse, download and visualize the data at the level of individual genes or entire studies.

NAR Database Issue 2011
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tagsanimals computational biology database management systems forecasting gene expression profiling genetic databases genome genomics humans information systems national library of medicine (u.s.) oligonucleotide array sequence analysis software design united states
setsNational Center for Biotechnology Information (NCBI)

NCBI Influenza Virus Sequence Annotation ToolTool Content

http://www.ncbi.nlm.nih.gov/genomes/FLU/Database/annotation.cgi

DNA > Annotations
DNA > Sequence Retrieval and Submission
Model Organisms > Other Organisms

The NCBI Influenza Virus Sequence Annotation Tool is a web application for user-provided sequences. It can predict protein sequences encoded by an input flu sequence and produce a feature table that can be used for sequence submission to GenBank.

NAR Web Server Issue 2007
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tagsalgorithms amino acid sequence dna sequence analysis genotype influenza a virus influenza b virus molecular sequence data sequence alignment viral dna viral genes viral genome viruses
setsNational Center for Biotechnology Information (NCBI)

NCBI Map ViewerTool Content

http://www.ncbi.nlm.nih.gov/mapview/map_search.cgi

DNA > Annotations
Human Genome > Annotations

The NCBI Map Viewer provides graphical displays of features on NCBI\'s assembly of human genomic sequence data as well as cytogenetic, genetic, physical, and radiation hybrid maps.

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tagsanimals biotechnology chromosome mapping gene expression profiling genes genetic databases genome humans mice molecular models phenotype sequence alignment sequence homology tertiary protein structure united states
setsNational Center for Biotechnology Information (NCBI)

NCBI Structure GroupResource Content

http://www.ncbi.nlm.nih.gov/Structure/

Protein > 3-D Structure Retrieval/Viewing

Good starting point with links to databases and tools.

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OMIMDatabase Content

http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=OMIM

Human Genome > Health and Disease

Online Mendelian Inheritance in Man; catalog of human genes and genetic disorders with descriptive text, references, and links to many NCBI resources including GenBank and PubMed.

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