It's often to show growth of sequence data of interest when one writes research proposal. For an example, you requires to collect number sequences from agricultural organisms and compare it to human if you want to explain how sequences regarding to agricultures grow faster than human data. Usually the gross statistics of GenBank, is posted on NCBI's Web page, might be not enough to describe details of the data growth.
To complete the above table, we need to count total records for each species in dbEST at current date. It's quite simple as the following: 1) choose a database, EST, on NCBI's front page; 2) press search button; 3) click advanced search; 4) choose an "Organism" field; 5) type "human" on query box; 6) click show index; 7) press "add to Search Box"; 8) press preview button (not search here), and 9) repeat for every species from 3).
By using show index, preview, and limit functions in Entrez, you can quickly collect meta information like number of entries.
dbEST | Total records | Records for last 3 years | Growth rate for last 3 years |
human | 8,315,231 | 177,492 | 2.1% |
mouse | 4,853,547 | 3,289 | 0.1% |
cattle | 1,559,494 | 45,232 | 2.9% |
pig | 1,620,570 | 144,207 | 8.9% |
chicken | 600,423 | 1,041 | 0.2% |
insects | 4,493,137 | 1,864,326 | 41.5% |
bacteria | 1,266 | 1,012 | 79.9% |
fungi | 2,893,583 | 1,508,814 | 52.1% |
plant | 22,633,681 | 7,290,397 | 32.2% |
To complete the above table, we need to count total records for each species in dbEST at current date. It's quite simple as the following: 1) choose a database, EST, on NCBI's front page; 2) press search button; 3) click advanced search; 4) choose an "Organism" field; 5) type "human" on query box; 6) click show index; 7) press "add to Search Box"; 8) press preview button (not search here), and 9) repeat for every species from 3).
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| Select DB of interest |
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| In advanced search |
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| Now you can validate your query word whether correct term in Entrez and then choose "human (10064832)" among drop items. |
Here the number in parenthesis means number of entries for human organism. Please try yourself to choose "All fields" and same query, then compare the numbers. Maybe they are different counts, why?
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| One query was built and the results was stored as #4 symbol in Search History. |
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| With repeats for every species, you can get similar results like the above. |
Now we need to find whole numbers of EST for last 3 years. At first back to front page of dbEST and the click the limits link. Now you can see the following screen and choose proper items in "Published in the last", and then press search button. When you see a list page of results, click "advanced search" again. If you see similar page like the below, it's correct.
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| In this page, #11 query means total numbers of ESTs published for the last 3 years |
To find human ESTs published for the last 3 years, you better to use an "AND" Boolean operator with shortcut symbol. That means to type query as the following then push the "Preview" button.
By repeating for every organisms, you might get similar results like the below. The growth rates for each organisms should be calculated by your self.
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