Workshop (II)

Good morning! You have attempted to submit jobs in batches last night and the computer worked very hard for you at night. Presumably, the results are ready for analysis by now. Please analyze your results in the following aspects:

  1. Connect to GeneMark (GeneMark at EBI) and submit your seq for analysis. (use your own E-mail address to receive the graphic representation.)
  2. Use your seq. as a query to submit a blastn job (use nucleic acid to search nucleic acid database) to GCG
  3. FTP your blast results back to PC and store them under tblastn subdir
  4. Go to subdir , open genome_ide.xls => Select the main item "ORF File Util", then select "Import ORFx blast"
  5. Now you will be able to view your blast results from this Excel table. Alternatively, you can use VisualBlast (we will not teach how to use this software until the 3rd day) to examine the tblastn files one by one.
  6. Please make a preliminary assignment based on your blast results, and fill it in the column labeled as "Similar to ... (tblastn)". If there is no matche, label it as "none".
  7. Create a subdirectory call "tblastn" in FTP to . Transfer all your tblastn file to this new subdir.
  8. Transfer your POST file to FTP to
  9. Please submit your seq. for tRNA scan (a local example of tRNA scan)
  10. Please compare the rRNA sequences (query) against your seq (databank) using FastA.

Examples used in the class

  1. Results of ORF analysis of the test.xls
  2. Results of tRNA scan