Contact developer File a bug or feature request                                                     RSS


Screenshots

Plasmi::db in action

Sample Image

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.

Sample Image

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....

Sample Image

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
Sample Image

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