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Retrieving sequence data from Entrez



In this exercise, user can learn how to use Entrez search engine and its associated databases. 


1. Please follow the steps given in simulator tab to open home page of Entrez in your web browser. Which look the same as showed in Figure 1.

Figure 1: Home Page of Entrez


2. User can type any query word in the query box, which will display the list of results associated with that query from all the databases in Entrez. Here in this example the user searches for “insulin” as shown in Figure2.

Figure 2: Search across databases using Entrez


3. The results are displayed with their corresponding number of records (hits) on the left side in rectangular boxes with a short description about each database.

Figure 3: Search results displaying the number of records.


4. Select any database which will display sequence records. Here in this example, the user selecting “Nucleotide” database by clicking on the hyperlink of Nucleotide as shown in Figure 4.


Figure 4: Selecting the Nucleotide database


5. The result page displays the nucleotide database records for different organisms with different features. The selected database will give a message on the top of the page with database name and their corresponding number of records. Along with nucleotide records, it also gives information on EST (Expression Survey Sequence) and GSS (Genome Survey Sequence) as shown in Figure 5.


Figure 5: Displaying the number of records for Nucleotide sequences with EST and GSS


6. The results are displaying with their unique Accession Number and Gene ID number for nucleotide with a short description of number of base pairs. User can filter his results according to their preference by clicking on the “Filter your results” option.


7. User can select a specific organism by selecting on the “Top Organisms” which is displayed on the right side of the result page with their corresponding number of records as shown in Figure 6.


Figure 6: Result Page displaying the nucleotide records


8. The result is displayed in GenBank format, by default as shown in Figure 6. User can switch to FASTA format by clicking on the FASTA option which is displayed on the top. The FASTA format representation is shown in Figure 7 and 8.



Figure 7: Switch to FASTA format by clicking on the FASTA option 


Figure 8: Results displaying FASTA sequence format


9. User can select different tools on the right side of the FASTA sequence page which is giving options to analyze the sequence by performing BLAST, Pick Primers, and Highlight Sequence Features (Figure 9). Selecting these features will redirect it to their homepage from the NCBI website. User can find different articles, associated pathways, Reference Sequence information based on the respective nucleotide of interest.

Figure 9: Displaying different tools to anlyze the sequence data


10. User can select “Display Settings” as Graphics which will display records in its Graphical representation (Figure 10).

Figure 10: Graphical representation of the sequence data


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