Tag Archives: blast

Fifth lab: pick your primers

Today we’ll meet at 1.30 pm in aula F pr to finish together our “pick-primers.pl” program. During last lab most of you got Primer3 running with our custom parameters. Primer3 output consists in a list of possible primer pairs.

We want to blast each primer against reference contigs to check how many sequence similar to it are present in the genome. This is a pivotal test to have specific PCRs. To make this we design a subroutine called ‘blast’ that takes as input a sequence (primer) and blast it against the contigs and parses the output returning a list of hints. In particular we consider dangerous those aligment long as the query -2 bp. Thus if our primers is long 20 and the match is 15 we will discard it. If the match with another contig is 18 bases long, we will report this to the user.

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Parse BLAST output (tabular format)

We performed a BLAST aligment using the -m 8 parameters, that produces a tabular format.
Let’s review how to parse it with Perl.

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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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