HUSAR Bioinformatics Lab
Deutsches Krebsforschungszentrum Department of Molecular Biophysics
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Open print version HUSAR Bioinformatics Lab :: Documentation :: Online Exercises 
Online Exercises of the Introductory Course to HUSAR at DKFZ:
 
Content:
  1. First steps in simple mode
  2. First steps in advanced mode
  3. First steps in command line
  4. First steps in SRS
 
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1. First steps in simple mode

  1. Create a subdirectory of the directory workshop. Name it Myproject. Specify this new directory as your current working directory.

  2. Fetch sw:P08168 and save the sequence file in your directory Myproject. Try to find similar regions to the remote sequence sw:P10523.

  3. Use the program mapsort to compute a restriction enzyme map of the remote sequence embl:A02710. Choose parameters circular and output format tick-style for this application. Use your own local data file myenzyme.dat. Run the application plasmidmap with the data obtained from mapsort.

  4. Select the application primer. Find primers to amplify the CDS of the green fluorescent protein of the sequence vector:U19276. Verify, that the chosen primers bind only to the desired positions within the whole vector sequence.

  5. View the results and remove the result files from the Result page. Leave no traces. Delete files and directory Myproject.

 
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2. First steps in advanced mode

  1. Use remote sequence X92495 from the EMBL database. Carry out a BLASTN2 search with X92495 against the database primate. You can continue with another exercise while waiting for the result.

  2. With the application BL2SEQ, first compare the sequences sw:2a5d_human and sw:2a5d_rabit then sw:2a5d_human and sw:2a5e_rabit. What is the difference? Make sure to use the correct writing.

  3. What is the isoelectric point of the protein p00001 from the swissprot database?

  4. Create a multiple alignment using Clustal on all swissprot-entries starting with hba1_ Use the resulting msf-File to predict secondary structures of proteins (dsc).

  5. Try to find out something about em_vi: U72030 concerning the localization of origins, exons, introns.

  6. Use the aminoacid-sequence sw:LRP1_human to search it against the protein database Swissprot on our bioccelerator (there it will perform an accurate Smith-Waterman search) When using the bioccelerator directly via our homepage do not log in and choose run mode 'interactive'; within HUSAR use: sw_bic.

  7. a. Create a small search set consisting of all bacterial entries from the EMBL database, the local sequence X70276 (in your directory) and all database entries starting with 'ze'.
    b. Carry out a FASTA search with X70276 against this search set. Which sequence has the best score ?

 
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3. First steps in command line

  1. Add CGATGGCTAG to the end of the sequence exercise1.seq which is in your subdirectory workshop.

  2. How many restriction enzymes cut this sequence just one time?

  3. Fetch the remote sequence embl:J02647. Include the nucleotides 50-100 of the fetched J02647.em_om at position 10 in the sequence exercise1.seq.

  4. Compare the sequence exercise1.seq with J02647.em_om using similarity.

  5. Remove the results of map and similarity.

 
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4. First steps in SRS

  1. Search SwissProt for entries concerning the cebb (ccaat/enhancer binding protein beta). Which Prodom entries are linked to the SwissProt sequence cebb_mouse?

  2. Look for rat cathepsin sequences in Swissprot . Which of those are structurally resolved proteins?

  3. Look for rodent but not rat cathepsin sequences in Swissprot. Save those entries, import them into W2H and build a multiple alignment.

  4. Can you find the complete coding sequence for the human transcription factor TFIIIB-90?

  5. Which information contains the OMIM database? Search OMIM with keyword BRCA.

 
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