Hi Divya,

primer design for STR (I suppose it stands for short tandem repeats) is the same as for regular PCR - you can try any of online tools - Primer3 is a good one: http://bioinfo.ut.ee/primer3-0.4.0/

Make sure, your primers span the polymorphic region (one primer upstream, the other downstream of repeats). It is important thatyour primers do not anneal to repetitive sequence. 

The optimal length of PCR product should be rather shorter - lets say starting from 100bp (when number of repeats is in the lower expected range) - that improves the resolution.

Depending on the size of repetitions, amplified fragments are to be separated using agarose gel (for long repeats only - say 10 bp and more) or a capillary sequencer (for shorter repeats). When sequencer is to be used, one primer should be fluorescently labeled. Make sure, you do not use Taq polymerase (it adds extra bases -dA). Proofreading polymerase capable of creating blunt ended PCR products is needede (such as Pfu, etc).

Martin

Hi Divya

I guess Martin's answer is good enough for the primers design question (although many of us are OK using normal Taq polymerase).

Regarding your haplotype question, haplotype analysis is very useful, for example, in genetic mapping. But it is most useful in LD mapping (association mapping). One fairly simple reason is that if you have haplotypes instead of genotypes, the number of observations in each of the LD matrix cells will increase, therefore making your estimations more statistically sound.

Can I ask why have you decided to go into haplotype analysis without knowing why is it useful?

Pablo

Look here for the ready desighned STR primers of STR loci.

http://www.cstl.nist.gov/strbase/str_fact.htm

Hi

In the following URL (cybertory.org) gives exercise of PCR Primer Design, verified, hope help you.

http://www.cybertory.org/exercises/primerDesign/

Ayad

thank you all 

hai pablo  why i studied means we analyse mucolipidosis disorders  of patients . in  20  mutations i got 6 similar mutations (means in exon 19 tc deletion occures in all 6 mutation)  .so we go for STR analysis of exon -19