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Plasmi::db in action

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Figure 3.

One persistent problem for molecular biologists is the verification of primer sequences.

Why did I order these primers anyway? Do they encode the desired sequence? Can I check a set of primers easily? What is its Tm?

Using in-line dynamic 6-frame translation, each primer can be checked at a click of a button.

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Figure 4.

Calculation of stats for a protein is painful.

"If I add a His-tag and TEV cleavage site to my protein, what will be the molecular weight?"

Just enter in the DNA sequence and it will be dynamically translated and its stats calculated....

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Figure 5.

I need primers corresponding to each of the 32 proteins I work on. How can I design them all before I pick up the kids?

Aaagh! I've just bought these primers with NdeI sites in them, and I've got an NdeI site in my gene! I forgot to check the restriction pattern- my boss will kill me!

By using a tailor-made primer designer, you can:

  • Select primers which will have appropriate Tms
  • Specify sequences to add to the 5' and 3' primers
  • Have restriction digests performed automagically to make sure there are no NdeI sites (or any other enzyme sites!) in your gene
  • Translate your primers dynamically (of course, you get the picture now?!), to make sure there isn't a stop codon before your His-tag
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Figure 6.

Standard plasmids are stored in a table, with PDF files listed with them.

// This makes a new Dna object from a string 
$oPcr = new Dna($sPcr) ;
// Dna objects have a "len" method 
print "The length of the PCR product is" . $oPcr->len() . "bp";
$oProt = $oTranslator->translatetoStop($oPcr);
print "The protein is: "$oProt->len() . "residues, and is ". $oProt->molWt() . " Da.";
print $oProt->pretty();
// The getData() method gets the sequence as a string from a sequence object
$sPcr = $oPcr->getData();
// Remove stop codons
$sPcr = SeqUtils::StripStop_($sPcr); 
// Remove iMets
$sPcr  = SeqUtils::StripIMet_($sPcr);
$aPrimers  = SeqUtils::DesignPrimerPair_($sPcr,15,25,45,75);

Figure 7.

Are you intersted in doing more? The syntax for sequence manipulation is easy, as an improved version of BioPHP