CLASS 23. Biology WorkBench and CAMERA.

PART 1. Prediction of transmembrane helices in a protein.

INSTRUCTIONS:

For each exercise, provide search query used and keep the answers brief. Email me the answers by Sunday 11:59PM AST at the latest.

Use "CLASS 23 EXERCISE" as a message subject, and type answers directly to email body (i.e., no document attachments please). Make sure that first line of your message is your NAME.
LINKS

  1. Open an account at the Biology workbench .  The Biology WorkBench is a web-based tool for biologists. The WorkBench allows biologists to search many popular protein and nucleic acid sequence databases. Database searching is integrated with access to a wide variety of analysis and modeling tools, all within a point-and-click interface that eliminates file format compatibility problems.

  2. Import the sequence into the workbench:

    a) Log into the workbench

    b) Select PROTEIN tools (note that you can toggle between styles of buttons and menus [3 styles] by clicking on the Biology Workbench banner at the top of the page).

    c) Select the program that allows to add a protein sequence (you need to click on "Run" button to start the program)

    d) Upload the sequence encoding the bacteriorhodopsin (GI: 15826249) into the appropriate form field and add a label name. Click Update, and then Save.

  3. Bacteriorhodopsin is a membrane protein whose crystal structure is known. If you want to explore the structure go to PDB ( here ). Search for 1JGJ and glance at structure. Alternatively, explore the structure at NCBI (linked to GI: 15826249)

  4. Perform some analyses with bacteriorhodopsin sequence: In the biologist's workbench, select the bacteriorhodopsin molecule and run the programs GREASE and TMHMM on this sequence (both programs predict the transmembrane spanning helices regions of a sequence). Compare the results with the annotation in the Genbank record for bacteriorhodopsin (GI: 15826249). How well does the prediction of membrane spanning helices work? [check info on hydropathy profile and pp. 208-211 in your textbook].

PART 2. Exploring CAMERA database

  1. Open an account on CAMERA web site.

  2. Retrieve a proteorhodopsin from GenBank (accession number AAY78592).

  3. In CAMERA, do an advanced BLAST search with proteorhodopsin sequence as a query. Use "GOS: All metagenomic sequence reads (N)" as a database. Increase "db alignments per query" to 500. Submit the job (#1). While the search is pending, submit the same BLAST search with "ChickenCecum" as a database (#2). Compare the results. Did you find any significant results in job #2? Why or why not? In what georgaphic regions do you find proteorhodopsins? Explore sequence alignments for individual BLAST hits. What can you say about the data in GOS database based on these search results?