2 replies to this topic

[mik77]

Hi,

I am new here and need some help please.
I would like to design a nested or hemi-nested  BSP for the following sequence:

BISULFITE MODIFICATION OF DNA

CGTCGGATGTGGTAAAAGTGACGTTTTTGGTGTGCGTCGGTGTATACGGGAAGTGATAATTTTCGCGCGGTTTTAGGCGG
ATGTTGTAGTAAATTTGGGCGTAATTAAGTAATGTTTGGTTATTTTCGCGGGAAAATTGAATAAGAGGAAGTGAAATTTGA
ATAATTTTGTGTTATTTATAGCGCGTAATATTTGTTTAGGGTCGCGGGGATTTTGATCGTTTACGTGGAGATTCGTTTAGG
TGTTTTTTTTAGGTGTTTTTCGCGTTTCGGGTTAAAGTTGGCGTTTTATTATTATAGTTAGTTGACGCGTAGTGTATTTAT
ATTCGGTGAGTTTTTTAAGAGGTTATTTTTGAGTGTTAGCGAGTAGAGTTTTTTTTTTCGAGTCGTTTCGATATCGGGATT
GAAAATGAGATATATTATTTGTTACGGAGGTGTTATTATCGAAGAAATGGTCGTTAGTTTTTTGGATTAGTTGATCGAAGA
GGTATTGGTTGATAATTTTTTATTTTTTAGTTATTTTGAATTATTTATTTTTTACGAATTGTATGATTTAGACGTGACGGT
TTTCGAAGATTTTAACGAGGAGGCGGTTTCGTAGATTTTTTTCGAGTTTGTAATGTTGGCGGTGTAGGAAGGGATTGATTT
ATTTATTTTTTCGTCGGCGTTCGGTTTTTCGGAGTCGTTTTATTTTTTTCGGTAGTTCGAGTAGTCGGAGTAGAGAGTTTT
GGGTTCGGTTTTTATGTTAAATTTTGTGTCGGAGGTGATCGATTTTATTTGTTACGAGGTTGGTTTTTTATTTAGTGACGA
CGAGGATGAAGAGGGTGAGGAGTTTGTGTTAGATTATGTGG

Methyl primer express gave me these primers:

F:5' TTTAGGTGTTTTTTTTAGGTGTT 3'
R1:5' AAAAAATTATCAACCAATACCTCT 3'  
R2: 5' AAAAAATAAATAAATCAATCCCTT 3'  

Are they any good.

Thanks

[methylnick]

in my experience, methyl primer express does a really good job of designing good bisulphite pcr primers when left at default settings. Like all primer prediction programs it is just really that, it will give you the best primers given the set parameters you tell it.

As to whether your designs are good or not, you have to try them out to find out.

[mik77]

methylnick, on May 18 2010, 06:32 PM, said:

in my experience, methyl primer express does a really good job of designing good bisulphite pcr primers when left at default settings. Like all primer prediction programs it is just really that, it will give you the best primers given the set parameters you tell it.

As to whether your designs are good or not, you have to try them out to find out.

Thanks methylnick I have tried them and they are ok