BLAST Exercise: Detecting and Interpreting Genetic Homology

default behavior under “Return Format” is “tar file.” This option means that RepeatMasker will
return the results of our search as a compressed archive file. Click “Submit Sequence”.
Depending on how busy the server is, the analysis may take a while (Figure 3).
Figure 3. Waiting for results from our RepeatMasker analysis
Figure 4. Download results from the RepeatMasker web server
The results page shows a summary of the RepeatMasker analysis. Click on the link “Masked
sequence and matches in compressed format” (below the header) to download the archive file
containing the results of the RepeatMasker analysis onto your computer (Figure 4).
Typically, you can expand the archive file simply by double-clicking the file. You can also
expand the archive by using gunzip and then untar the file. You can also use other programs that
can process tar gzip files (ie. StuffIt Expander, Winzip). For this tutorial, you can expand the
archive file simply by double-clicking the file.
Once you have expanded the archive file, you should have a folder with several useful files:
o A copy of the original sequence with its repeats replaced by Ns, in a file ending with the
extension “.masked”
o A summary of the repetitive elements found in the sequence, in a file ending with “.tbl”
o A detailed list of repetitive elements found, in a file ending with “.out”
Question 2: How many repetitive elements does our sequence contain, and what
are their types (Hint: examine the “.tbl” file.)
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