[Gmod-help] gbrowse_syn

[Shao, Jonathan]

Sheldon McKay,

 

My name is Jonathan Shao and I believe I met you at PAG.  I saw your
demo and  I am trying to implement the gbrowse_syn program.

 

How do I generate meaningful clustal alignments?

 

case 1: have contigs and want to align them to a completed genome

Do you blast the contigs against the completed genome and then use
clustalw on that isolated region?

 

 

case2: align 2 completed genomes

Do you slice/cut up one of the completed genomes into defined sequence
lengths and blast each sequence against a completed genome?

 

Is blast the method of choice or are that other programs that would be
better for aiding in creating the alignments for clustalW?

 

 

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Do you have sample data with corresponding contig files that I can work
with? I did see the wormbase gbrowse_syn, but I am not sure how you
generated the alignments. Also, I did not see a sample config file for
gbrowse_syn. 

 

 

Any advice you can give me would be appreciated.  

 

Thanks in advance,

 

Sincerely,

Jonathan Shao 

 

 

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