[Gmod-help] Genomic Gap Closure

[Schwartz, Stephanie (CDC/CCID/NCIRD)]

Good Morning,

I was referred here from the folks at Open Helix, who said you may be
helpful in providing guidance as to strategies for genomic gap closure.
I have a prokaryotic genome assembly with approximately 10 gaps.
Unfortunately each gap is flanked by repetitive elements dispersed
throughout the genome, and I cannot design specific primers for those
gaps for PCR and sequencing.  Most primers designed in the context of
the gaps will bind to multiple loci.  I have tried numerous things,
including projector 2 (open source tool).  Can you recommend any tools,
strategies, or experts in the field who may be willing to help or
provide guidance?  Thank you.

Sincerely,

Stephanie Schwartz
CDC, Div. of Bacterial Diseases
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