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.
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
<-=-*******************
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