primer design - microalgae (Jun/14/2011 )
please help me...
i need to design a primer for micro algae to identify their species
how can i design a primer??
1) you find a gene / region specific for your algae.
2) use primer3 to design the primer.
You can try to check previous primer from previous studies in related journal
But to design your own primer, and just like what Adrian said need to check the specificity of the gene u need to amplify...go to gene bank (eg; NCBI) and To design the primer u can use oligonucleotide calculator..just google it, make sure the each primer is good specificity (18-30bp), no predicted hair pin, good percentage of GC content (40%-50%), make sure u have the good predicition Tm for your primers..all now easier using software...there are many free software there but i use oligonucleotide calculator...after you design that primers try to blast the primer to check the specfic binding
The easy one just try to use same primers that were used by other people in order to check their algae species...i think there must be conserve region that applicable for all type of algae...In bacteria we use 16sRDNA primers to identify the species, applicable to all bacteria so try to check what primers normally people used to identify your algae species