CS Mukhopadhyay and RK Choudhary
School of Animal Biotechnology, GADVASU, Ludhiana
The NCBI nucleotide database (http://www.ncbi.nlm.nih.gov/nucleotide/) is an archive of gene, transcript, and fragments of genomic DNA sequences. It combines several online public repositories, including GenBank (the genetic sequence database of NIH), RefSeq (annotated, non‐redundant reference sequence from genomic, transcript and protein), TPA (third‐party annotated data on nucleotide sequences), and PDB (protein databank: a repository of 3D structures of proteins and nucleic acids). The International Nucleotide Sequence Database Collaboration (INSDC) maintains the liaison between the three major molecular data repositories – namely, NCBI, DDBJ, and EMBL – to share the nucleotide data present in any of those databanks.
A brief description of the NCBI databases has been given in Appendix A “NCBI Database: A Brief Account” at the end of this book.
To search and download nucleotide sequences from NCBI Nucleotide database and save as a text file (*.txt). The sequence of interest for downloading could be complete or partial gene/mRNA/coding sequence, non‐coding RNA (rRNA, tRNA), non‐coding and repeat sequences (VNTR) in the genome, partial genomic DNA sequences, and so on.
One can search other NCBI databases that archive nucleotide sequences:
The user can narrow down the search by using the parameters available after clicking on the hyperlink “Limits”. However, NCBI has removed this option nowadays. The available options are:
Click on the hyperlinked word “Advanced” just below the text box. The new page enables you to build your search settings.
Please note that the search builder enables us to specify the keywords according to their type (i.e., accession, assembly, author, journal and so on); in turn, this instructs the search engine to pinpoint the keywords from the database, depending on its feature or type.
Let us take our previous example: “Drosha Bos taurus”. In the search builder, click on the drop‐down menu (shown as “All Fields”) and select “Gene Name” and type “Drosha”. The role of “Show index list” is discussed in the next paragraph. Next, click on the drop‐down list of the second‐row field and select “Organism” and then type “Bos taurus” (without quotes). If you have more keywords, then add more rows accordingly, and select the specific field before typing the keyword(s).
The “Show index list” button will show the list of indexes from which you can specify your index. To move further along the index, you can use “Previous 200” or “Next 200” options. The “+” and “–” symbols beside each of the text boxes allow you to add (new) or delete the corresponding text boxes.
Please note that we can also do the advanced search without using the “Advanced Search Builder”. Type the keywords in the form as given below: “term [field] OPERATOR term [field]”. So, in the case of our current example, it will be:
Drosha[Gene name] AND Bos taurus[Organism]
18.217.198.254