[BiO BB] help!

[shivam srivastava]

Hi! 
I'm into a short project (domain problem).
To find out unique conserved region among conserved regions of genomes in 
evolution 
right from very primitive species to highly advanced species using internet 
& public databases as the working platform
 The results would include 
>DNA seq. of Unique conserved region & protein seq if available
>SNPs identified in the unique conserved region
 What"ll be the likely approach to this problem with respect to the tools .
Should i go for similarity search or identity? multiple or global alignment 
& which level of genome (transcriptome/mRNA) should i work with?
I'll be highly thankful for ur guidance
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