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Page 1 Biological sequence database: NCBI 23 Taxonomy: This database was conceptualized and became functional in 1991 contains curated hierarchical taxonomic information about organisms for which sequence information is available at the public database. In addition to being a portal to taxonomy, the site also provides birds-eye-view of the resources associated with a specific organism in question. The taxonomic classification is based on a combination of molecular data and morphological data and can be accessed at http://www.ncbi.nlm.nih.gov/taxonomy. Figure: Taxonomy database with complete taxonomic details of an organism (taxon specific page) Source: http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=9606&lvl=3&l in=f&keep=1&srchmode=1&unlock Page 2 Biological sequence database: NCBI 23 Taxonomy: This database was conceptualized and became functional in 1991 contains curated hierarchical taxonomic information about organisms for which sequence information is available at the public database. In addition to being a portal to taxonomy, the site also provides birds-eye-view of the resources associated with a specific organism in question. The taxonomic classification is based on a combination of molecular data and morphological data and can be accessed at http://www.ncbi.nlm.nih.gov/taxonomy. Figure: Taxonomy database with complete taxonomic details of an organism (taxon specific page) Source: http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=9606&lvl=3&l in=f&keep=1&srchmode=1&unlock Biological sequence database: NCBI 24 Figure: Taxonomy database hierarchical display page Source: http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi Table : A summary list of taxa represented in taxonomy database as on December 2012 Ranks: higher taxa genus species lower taxa total Archaea 115 131 466 0 712 Bacteria 1209 2286 11268 770 15533 Eukaryota 18913 59886 251517 19045 349361 Fungi 1365 4111 25496 981 31953 Metazoa 13767 39148 117739 9513 180167 Viridiplantae 2292 14058 100061 8320 124731 Viruses 575 378 1974 0 2927 All taxa 20838 62689 265258 19815 368600 Source: http://www.ncbi.nlm.nih.gov/Taxonomy/taxonomyhome.html/index.cgi?chapter=statistics& uncultured=hide&unspecified=hide PubChem: NCBI provides a database service, PubChem (setup in 2004), that stores curated information about description, structure and bioassay of a range of small molecules that have a role in biological priocesses. PubChem Compound, for example, is a database Page 3 Biological sequence database: NCBI 23 Taxonomy: This database was conceptualized and became functional in 1991 contains curated hierarchical taxonomic information about organisms for which sequence information is available at the public database. In addition to being a portal to taxonomy, the site also provides birds-eye-view of the resources associated with a specific organism in question. The taxonomic classification is based on a combination of molecular data and morphological data and can be accessed at http://www.ncbi.nlm.nih.gov/taxonomy. Figure: Taxonomy database with complete taxonomic details of an organism (taxon specific page) Source: http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=9606&lvl=3&l in=f&keep=1&srchmode=1&unlock Biological sequence database: NCBI 24 Figure: Taxonomy database hierarchical display page Source: http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi Table : A summary list of taxa represented in taxonomy database as on December 2012 Ranks: higher taxa genus species lower taxa total Archaea 115 131 466 0 712 Bacteria 1209 2286 11268 770 15533 Eukaryota 18913 59886 251517 19045 349361 Fungi 1365 4111 25496 981 31953 Metazoa 13767 39148 117739 9513 180167 Viridiplantae 2292 14058 100061 8320 124731 Viruses 575 378 1974 0 2927 All taxa 20838 62689 265258 19815 368600 Source: http://www.ncbi.nlm.nih.gov/Taxonomy/taxonomyhome.html/index.cgi?chapter=statistics& uncultured=hide&unspecified=hide PubChem: NCBI provides a database service, PubChem (setup in 2004), that stores curated information about description, structure and bioassay of a range of small molecules that have a role in biological priocesses. PubChem Compound, for example, is a database Biological sequence database: NCBI 25 that stores information about validated structures of small chemical compounds; and PubChem BioAssay contains data about bioactivity or bioassay performed with the chemical compound. The PubChem database also reveals the biosynthesis and/or role of the chemical compound in various metabolic pathways by providing links to database of metabolic pathways such as KEGG/BioSystems. Figure : Access to PubChem databases through Entrez gateway Source: http://www.ncbi.nlm.nih.gov/sites/gquery Page 4 Biological sequence database: NCBI 23 Taxonomy: This database was conceptualized and became functional in 1991 contains curated hierarchical taxonomic information about organisms for which sequence information is available at the public database. In addition to being a portal to taxonomy, the site also provides birds-eye-view of the resources associated with a specific organism in question. The taxonomic classification is based on a combination of molecular data and morphological data and can be accessed at http://www.ncbi.nlm.nih.gov/taxonomy. Figure: Taxonomy database with complete taxonomic details of an organism (taxon specific page) Source: http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=9606&lvl=3&l in=f&keep=1&srchmode=1&unlock Biological sequence database: NCBI 24 Figure: Taxonomy database hierarchical display page Source: http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi Table : A summary list of taxa represented in taxonomy database as on December 2012 Ranks: higher taxa genus species lower taxa total Archaea 115 131 466 0 712 Bacteria 1209 2286 11268 770 15533 Eukaryota 18913 59886 251517 19045 349361 Fungi 1365 4111 25496 981 31953 Metazoa 13767 39148 117739 9513 180167 Viridiplantae 2292 14058 100061 8320 124731 Viruses 575 378 1974 0 2927 All taxa 20838 62689 265258 19815 368600 Source: http://www.ncbi.nlm.nih.gov/Taxonomy/taxonomyhome.html/index.cgi?chapter=statistics& uncultured=hide&unspecified=hide PubChem: NCBI provides a database service, PubChem (setup in 2004), that stores curated information about description, structure and bioassay of a range of small molecules that have a role in biological priocesses. PubChem Compound, for example, is a database Biological sequence database: NCBI 25 that stores information about validated structures of small chemical compounds; and PubChem BioAssay contains data about bioactivity or bioassay performed with the chemical compound. The PubChem database also reveals the biosynthesis and/or role of the chemical compound in various metabolic pathways by providing links to database of metabolic pathways such as KEGG/BioSystems. Figure : Access to PubChem databases through Entrez gateway Source: http://www.ncbi.nlm.nih.gov/sites/gquery Biological sequence database: NCBI 26 Figure : PubChem Compound database allows users to browse and download information about the structure, function and cellular biosynthesis / role of small molecules Source:http://www.ncbi.nlm.nih.gov/pccompound/?term=Vincristine ;http://pubchem.ncbi.nlm.nih.gov/summary/summary.cgi?cid=5978&loc=ec_rcs http://www.ncbi.nlm.nih.gov/biosystems/148659?Sel=cid:5978#show=smallmolecules Page 5 Biological sequence database: NCBI 23 Taxonomy: This database was conceptualized and became functional in 1991 contains curated hierarchical taxonomic information about organisms for which sequence information is available at the public database. In addition to being a portal to taxonomy, the site also provides birds-eye-view of the resources associated with a specific organism in question. The taxonomic classification is based on a combination of molecular data and morphological data and can be accessed at http://www.ncbi.nlm.nih.gov/taxonomy. Figure: Taxonomy database with complete taxonomic details of an organism (taxon specific page) Source: http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=9606&lvl=3&l in=f&keep=1&srchmode=1&unlock Biological sequence database: NCBI 24 Figure: Taxonomy database hierarchical display page Source: http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi Table : A summary list of taxa represented in taxonomy database as on December 2012 Ranks: higher taxa genus species lower taxa total Archaea 115 131 466 0 712 Bacteria 1209 2286 11268 770 15533 Eukaryota 18913 59886 251517 19045 349361 Fungi 1365 4111 25496 981 31953 Metazoa 13767 39148 117739 9513 180167 Viridiplantae 2292 14058 100061 8320 124731 Viruses 575 378 1974 0 2927 All taxa 20838 62689 265258 19815 368600 Source: http://www.ncbi.nlm.nih.gov/Taxonomy/taxonomyhome.html/index.cgi?chapter=statistics& uncultured=hide&unspecified=hide PubChem: NCBI provides a database service, PubChem (setup in 2004), that stores curated information about description, structure and bioassay of a range of small molecules that have a role in biological priocesses. PubChem Compound, for example, is a database Biological sequence database: NCBI 25 that stores information about validated structures of small chemical compounds; and PubChem BioAssay contains data about bioactivity or bioassay performed with the chemical compound. The PubChem database also reveals the biosynthesis and/or role of the chemical compound in various metabolic pathways by providing links to database of metabolic pathways such as KEGG/BioSystems. Figure : Access to PubChem databases through Entrez gateway Source: http://www.ncbi.nlm.nih.gov/sites/gquery Biological sequence database: NCBI 26 Figure : PubChem Compound database allows users to browse and download information about the structure, function and cellular biosynthesis / role of small molecules Source:http://www.ncbi.nlm.nih.gov/pccompound/?term=Vincristine ;http://pubchem.ncbi.nlm.nih.gov/summary/summary.cgi?cid=5978&loc=ec_rcs http://www.ncbi.nlm.nih.gov/biosystems/148659?Sel=cid:5978#show=smallmolecules Biological sequence database: NCBI 27 Figure: PubChem Bioassay webpage snapshot Source: http://www.ncbi.nlm.nih.gov/pcassay/?term=Vincristine This section deals with databases that are specific to gene expression analysis and protein analysis, essentially biomolecules that are significant for “functionality” Databases-III: Expression analysis-GEO Proteins (Reference sequences, GenPept, UniProt/SwissProt, PRF, PDB, Protein clusters, Structure, UniGene, CDD):Read More
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FAQs on Lecture 5 - Biological sequence database: National Center for Biotechnology Information (PART 2) - Bioinformatics - Botany
| 1. What is the National Center for Biotechnology Information (NCBI)? |  |
Ans. The National Center for Biotechnology Information (NCBI) is a renowned database that provides access to a wide range of biological sequence information. It is a part of the United States National Library of Medicine (NLM) and is widely used by researchers, scientists, and students in the field of biotechnology and genomics.
| 2. How can I access the biological sequence database provided by the NCBI? | |
Ans. The biological sequence database provided by the NCBI can be accessed through their website. Simply visit the NCBI website and navigate to the "Databases" section. From there, you can select the specific database you are interested in, such as GenBank, RefSeq, or BLAST, and access the desired biological sequence data.
| 3. What are some of the key features of the NCBI biological sequence database? | |
Ans. The NCBI biological sequence database offers several key features that make it a valuable resource for researchers. These features include comprehensive coverage of genetic and protein sequences, integration with other NCBI databases, tools for sequence alignment and analysis, and the ability to search and retrieve specific sequences based on various criteria.
| 4. Can I submit my own biological sequences to the NCBI database? | |
Ans. Yes, the NCBI allows researchers to submit their own biological sequences to the database. This process is called sequence submission and requires following specific guidelines and formats. By submitting your sequences to the NCBI database, you contribute to the scientific community and make your data accessible to other researchers.
| 5. Are there any restrictions on the use of the biological sequence data from the NCBI? | |
Ans. The biological sequence data provided by the NCBI is freely available for research and educational purposes. However, there may be certain restrictions on the use of the data, especially when it comes to commercial applications. It is important to review and abide by the terms of use provided by the NCBI to ensure compliance with any restrictions or limitations on data usage.
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