[Bioperl-l] alignment and assembly

[Guoneng Zhong]

Hi,
I am trying to write an alignment function and an assembly function for 
dna sequences.  I looked at the the Bio::Align modules and am not sure 
how they can help me.  I am used to seeing two sequences align with bars 
indicating that nucleotide on the top sequence matches with that in the 
lower sequence.  Is there a tutorial or example like that on the site?

As for assembly, is there something like the TIGR Assembler that allows 
me to input two sequences and get hopefully one sequence out? 
(Obviously, I an make command line calls to TIGR Assembler, but perhaps 
a Bioperl interface?).

Thanks,
Guoneng