Wednesday, December 10, 2014

Gene Editor

The VD Editor is very good at making coding a faster and slicker process. I thought it to be time to make it an editor of genes, creating tools for analyzing sequences as well as ways of designing custom genomes. Here is how it works:

We start with some Jquery to handle the lightweight text operations, like switching out acronyms and words for protein sequences. First make some html:



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<body bgcolor = "#303030 ">


<script src="http://ajax.googleapis.com/ajax/libs/jquery/1.11.1/jquery.min.js"> </script>

<style>
  #sideBar { vertical-align:top;}
  #contentArea { vertical-align:top;}
</style>
<table>
  <tr>
    <td id="sideBar">
 
      </td>
    <td id="contentArea">
      
      
<textarea name="texty" id="field_id_29" rows="40" cols="100" style="color: #0086f7; background-color: black;font-weight: bold; font-family: source code pro; font-size:11; "></textarea>

Note the linking of the jquery source into the file. This demands that our application work online. I used this method for future cross platform building ease:

We can add some JS and JQ:

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         $("#field_id_29").bind("keyup", function() {
    var text = $(this).val();
    text = text.replace("alanine", "A" )
    $(this).val(text);
});

The above allows direct addition of amino acids into the sequence following using the Uniprot coding system.

Now for the big switcharoo:


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var capsacine_synthase="MIFILTVNFRWRYLILLICKSLMLLEISCPVKYPERFLGVCDTLIFRQTCLQEIFRGTCRICLSCFLLIFLTIVFPAKFRRVLVGFSSFSTFGSRIMTWLELCLRQLLTVRRWFIECLRKCYSRCYSSGNCCFTKASGDIFITYYSVWFFASFIVLQCFDLSSFPWDCSVGFQWVYGYCQARVSKMFYFLANFGSSTQPNTWCVSFDFDEQFCIDVVGRIVEFVLWENPKCHWELVEIGVTENGKQFIDRWSPVFDYELVQLEGSCSIRESNEGENSNVFRLSQKLEDIITGKKSVFGFHSFAFVKFD"

  $("#field_id_29").bind("keyup", function() {
    var text = $(this).val();
    text = text.replace("capsacine synthase", capsacine_synthase )
    $(this).val(text);
});

Now we employ VB for heavy text operations so integrate the js doc via a we bowser.  Before we start messing with whole genomes lets add a method to identify major sequences. this is the basic method:



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            buildbox.Text = Replace(buildbox.Text, "tata", "tataSTARTSTART")
Let's make sure we are online:



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   If My.Computer.Network.IsAvailable Then
            adder.ForeColor = Color.Green
            adder.Text = "Internet Connected"
        Else
            adder.ForeColor = Color.Red
            adder.Text = "Internet Disconnected"
        End If


And we load text files for large data segments such as the entire genome of synechocystis. And there you have it , a basic sketch of the gene editor. It willb e embedded int he next VD release.



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