Tag Archives: primer3

Second computer lab

After the brief introduction in class you are now ready to try by yourself a couple of command line programs: BLAST and Primer3.¬†After having worked with these tools, you’ll have some more time to play with Perl. Today we will

  • Practice again with the shell
  • Perform a BLAST via command line
  • Perl scripts
  • Primer3 test

Now our servers are set up and we can monitor your activity… so remember: read carefully, and type filenames exactly as we suggest.

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Try to close a gap

Here you are a simple homework to practice with Primer3 and our genome finishing goal.

Using the information stored in mate-paired reads, we see that the 5′-end of “contig05189” is linked to 3′-end of “contig01316”. Please note the 3′ and 5′ ends are indicated in gray boxes for each connection.

You can see that the path to the 3′ is a little bit more complex.

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