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Practice Constructing Queries, Part I: The Beginning

To see how the query process works, here is a beginning exercise:

0) Please create an account and begin a new session, if you have not already done so.

1) In the Biology Workbench, select "Protein Tools". You should arrive at a new page that contains a scroll menu.

2) Highlight "Ndjinn Multiple Database Search" from the scroll menu and then press the "Run" button. You should then be presented with a query field and a number of sequence databases, as well as genome databases.

3) Select the check buttons for the "PIR1" and "SWISSPROT" databases.

4) Type "myoglobin" in the object field and press the "search" button.

Practice Constructing Queries, Part II: Narrowing Your Search

You will observe that many objects were retrieved (204 at this writing).

Perhaps this includes some information you don't want, and you would like to automatically filter that information out, rather than inspecting it and discarding it manually. For example, suppose you only wanted to look at ape and human myoglobin, perhaps to discover which of the apes are our closest relatives. Now you can construct the search for "myoglobin AND (gorilla OR chimpanzee OR orangutan OR human)". Now when you press the "search" button, you will retrieve only a few sequences (28 at this writing).

Practice Constructing Queries, Part III: More Advanced Searches

Perhaps now you decide that basing a phylogenetic analysis on only one protein might be shaky, so you want to look at a second protein. Say you chose hemoglobin. You want to download data that will let you construct a phylogenetic tree among the apes with both hemoglobin and myoglobin and see if you get the same answer. This time construct the query as "(hemoglobin or myglobin) and (chimpanzee or gorilla or human or orangutan)." Now when you press the "submit" button you retrieve 90 entries (at this writing), all the hemoglobin or myoglobin entries for all the ape species that you asked for.

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