Note: all exercises were originally designed for use on a UNIX workstation. However, with slight modifications, they can be used on any other operating systems with Internet access.

EXERCISE 1. DATABASE SEARCHES

In this exercise, you will learn how to use several biological databases to retrieve information according to certan criteria. After learning the basic search techniques, you will be given a number of problems and asked to provide answers from the databases.

1. Use a web browser to retrieve a protein sequence of lambda repressor from SWISS-PROT (http://us.expasy.org/sprot/). Choose “Full text search in Swiss-Prot and TrEMBL.” In the following page, Enter “lambda repressor” (space is considered as logical operator AND) as keywords in the query window. Select “Search in Swiss-Prot only.” Click on the “submit” button. Note the search result contains hypertext links taking you to references that are cited or to other related information. Spend a little time studying the annotations.

2. In the same database, search more sequences for “human MAP kinase inhibitor,” “human catalase,” “synechocystis cytochrome P450,” “coli DNA polymerase,” “HIV CCR5 receptor,” and “Cholera dehydrogenase.” Record your findings and study the annotations.

3. Go to the SRS server (http://srs6.ebi.ac.uk/) and find human genes that are larger than 200 kilobase pairs and also have poly-A signals. Click on the “Library Page” button. Select “EMBL” in the “Nucleotide sequence databases” section. Choose the “Extended” query form on the left of the page. In the following page, Select human (“hum”) at the “Division” section. Enter “200000” in the “SeqLength >=” field. Enter “polya_signal” in the “AllText” field. Press the “Search” button. How many hits do you get?

4. […]