Talk:Synthetic Biology:Vectors/Barcode

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(Lookup Table approach instead)
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Is it useful to have a start and stop sequence to make sure that you have read all of the code?  Seeing as most of codon space is being used by the alphanumeric table you could add on an extra letter or number by accident if you didn't know either the length of the barcode or see a defined stop codon.  Not a problem in the short term but might crop up in the long run.--[[User:Bcanton|BC]] 16:25, 3 February 2006 (EST)
Is it useful to have a start and stop sequence to make sure that you have read all of the code?  Seeing as most of codon space is being used by the alphanumeric table you could add on an extra letter or number by accident if you didn't know either the length of the barcode or see a defined stop codon.  Not a problem in the short term but might crop up in the long run.--[[User:Bcanton|BC]] 16:25, 3 February 2006 (EST)
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== Lookup Table approach instead ==
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The current barcode approach assumes that a text string is adequate to represent the plasmid.
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For this to be true, you may need a universal naming approach. Since pSB1AC3 is not universally understood.
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An alternative approach is to use a lookup table on a known server (e.g. openwetware or the Registry)
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the advantages of this approach is that you can put much more information on the server and you can update
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the information after the part is in use. In fact, the code "pSB1AC3" only wokrs because there is a lookup
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table available at the Registry and openwetware. How about if someone in Iran created their own plasmid
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"pIRgH5x" how would you find what this was?
 +
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Once we agree on the lookup table, we could just have numbers encoded, or even have the DNA
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sequence itself generated uniquely. This would make error correction easier.
 +
 +
An advantage of this approach is that is would produce a much shorter barcode and sequencing reads that
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go farther into the part's sequence - [[User:Randy]RR]

Revision as of 12:33, 8 March 2006

What is the point of the vector barcode? Is it the same as (or a replacement for) the CDS barcode? Endy 13:06, 2 February 2006 (EST)

  • The vector barcode is designed to allow the user to "read" the name of the vector whenever they sequence a barcode containing plasmid with a verification primer (VF2 or VR). Currently, our vectors are indistinguishable from one another during sequencing. Some people have complained about this. I figured that the easiest way to create a plasmid barcode was to actually directly encode the name of the plasmid in the DNA. I am trying to make this code sufficiently general that any plasmid name could be encoded and that even system names could be encoded if we choose in the future. Thus, the plasmid barcode serves a slightly different purpose from the CDS barcode in that it is not necessarily designed to be an easy way to diagnose whether a piece of DNA has BioBricks CDSs in it. I welcome suggestions about a better way to do this. --RS
    • Reshma, thanks for this explanation. It seems like there are three different functions we could (should?) use barcodes for. First, for detection. Second, for identification. Third, for authentication. The original BioBricks barcode project was for detection. This project is (currently) for identification. I remember some discussions about moving the barcodes away from BioBricks and to the vectors themselves. Or, having barcodes as parts themselves. It would be nice to coordinate/get this right once and for all. If we can figure out what to do then we can propose something as a community-wide standard at SB2.0. Endy 18:28, 4 February 2006 (EST)

Is it useful to have a start and stop sequence to make sure that you have read all of the code? Seeing as most of codon space is being used by the alphanumeric table you could add on an extra letter or number by accident if you didn't know either the length of the barcode or see a defined stop codon. Not a problem in the short term but might crop up in the long run.--BC 16:25, 3 February 2006 (EST)

Lookup Table approach instead

The current barcode approach assumes that a text string is adequate to represent the plasmid. For this to be true, you may need a universal naming approach. Since pSB1AC3 is not universally understood.

An alternative approach is to use a lookup table on a known server (e.g. openwetware or the Registry) the advantages of this approach is that you can put much more information on the server and you can update the information after the part is in use. In fact, the code "pSB1AC3" only wokrs because there is a lookup table available at the Registry and openwetware. How about if someone in Iran created their own plasmid "pIRgH5x" how would you find what this was?

Once we agree on the lookup table, we could just have numbers encoded, or even have the DNA sequence itself generated uniquely. This would make error correction easier.

An advantage of this approach is that is would produce a much shorter barcode and sequencing reads that go farther into the part's sequence - [[User:Randy]RR]

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