17 January 2006

Past Projects (II)

After my PhD, I spent one year at the National Center of Genotyping based at Evry in the mass spectrometry team directed by Ivo Gut. The method for genotyping, called the GOOD-Assay used a primer extension of one base followed by a MALDI-TOF mass spectrometry, in multiplex.

c est moi qui l ai fait !


Here, I created a tool called SnipMachine used to find the best primers for this test according to the possible masses, the steric problems, the self/inter hybridization, etc... Here is an output.
strategy 1/10
-------------
 primer-list
 -----------
  copyprimer index("0")
  ---------------------
   Deletion 25-26
    SNP at position 25  ( can be  'A' 'C'  5'->3' )
   ------------------------------------------------
    if base base is "A" then mass ="1463"
    if base base is "C" then mass ="1439"

    mass-without-elongation : 1136
    sequence-name           : untitled sequence
    orientation             : Forward
    size                    : 22
    Tm                      : 69.8107
    charge-tag              : on base="A" mass="0" name="tag1"
    sequence
    --------
     5' GTAATCGATCGTAGCTAGCTaA 3'
  copyprimer index("1")
  ---------------------
    SNP at position 30  ( can be  'C' 'G'  5'->3' )
   ------------------------------------------------
    if base base is "C" then mass ="1483"
    if base base is "G" then mass ="1523"

    mass-without-elongation : 1180
    sequence-name           : untitled sequence
    orientation             : Reverse
    size                    : 20
    Tm                      : 71.1841
    charge-tag              : on base="A" mass="28" name="tag2"
    sequence
    --------
     5' AGTCAGCACTGAGCTACGaT 3'
  copyprimer index("2")
  ---------------------
    SNP at position 9  ( can be  'A' 'C' 'G' 'T'  5'->3' )
   -------------------------------------------------------
    if base base is "A" then mass ="1479"
    if base base is "C" then mass ="1455"
    if base base is "G" then mass ="1495"
    if base base is "T" then mass ="1470"

    mass-without-elongation : 1152
    sequence-name           : untitled sequence
    orientation             : Reverse
    size                    : 22
    Tm                      : 71.8038
    charge-tag              : on base="G" mass="0" name="tag1"
    sequence
    --------
     5' CAGTACGTACGATAGCTGATgA 3'

  Spectrogram
  -----------
   |
   |___ mass:1136 snp:0 (no elongation) seq:untitled sequence
   |
   |___ mass:1152 snp:2 (no elongation) seq:untitled sequence (+ 16)
   |
   |___ mass:1180 snp:1 (no elongation) seq:untitled sequence (+ 28)
   |
   |___ mass:1439 snp:0 base:C seq:untitled sequence (+ 259)
   |
   |___ mass:1455 snp:2 base:C seq:untitled sequence (+ 16)
   |
   |___ mass:1463 snp:0 base:A seq:untitled sequence (+ 8)
   |
   |___ mass:1470 snp:2 base:T seq:untitled sequence (+ 7)
   |
   |___ mass:1479 snp:2 base:A seq:untitled sequence (+ 9)
   |
   |___ mass:1483 snp:1 base:C seq:untitled sequence (+ 4)
   |
   |___ mass:1495 snp:2 base:G seq:untitled sequence (+ 12)
   |
   |___ mass:1523 snp:1 base:G seq:untitled sequence (+ 28)
   |

  melting-temperatures
  --------------------
   |
   |___ Tm:=69.8107  SNP:=0 on sequence:=untitled sequence
   |
   |___ Tm:=71.1841  SNP:=1 on sequence:=untitled sequence( +1.37339)
   |
   |___ Tm:=71.8038  SNP:=2 on sequence:=untitled sequence( +0.61974)
   |

  sequences
  ---------
   sequence:untitled sequence (63)
   -------------------------------
    ATCGTAATCGATCGTAGCTAGCTAActAGCsATCGTAGCTCAGTGCTGACTGACTCATCAGCT
       *******************-=->    <-=-*****************
   sequence:untitled sequence (45)
   -------------------------------
    ATCGTAATCnTCATCAGCTATCGTACGTACTGATCGATCGATCGT
             <-=-*******************

at

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