[BiO BB] Re: Comparing Whole Genome Sequences

[Tristan Fiedler]

The Blastz algorithm has been optimized for genome-scale alignments.  
Pre-processing of sequences to mask low complexity region, repeats, 
vector contamination, poor quality sequence, tandem repeats, etc may be 
needed however.

References :

http://pipmaker.bx.psu.edu/dist/blastz.pdf
http://www.pnas.org/cgi/content/abstract/100/20/11484

Cheers,        Tristan
---
Tristan J. Fiedler
Postdoctoral Fellow - Stein Lab
Cold Spring Harbor Laboratory
On Dec 21, 2005, at 12:01 PM, 
bio_bulletin_board-request at bioinformatics.org wrote:
>
>
> Message: 1
> Date: Tue, 20 Dec 2005 20:51:57 +0330
> From: "hamid" <hamid at ibb.ut.ac.ir>
> Subject: [BiO BB] Comparing whole genome sequences
> To: bio_bulletin_board at bioinformatics.org
> Message-ID: <WorldClient-F200512202051.AA51570064 at ibb.ut.ac.ir>
> Content-Type: text/plain
>
> I want to compare (align) whole genome of several organisms. How can I 
> do
> that? there are several tools such as mVISTA that can align multiple
> preprocessed sequences but I want to compare my own organisms. for 
> example
> if I want to compare 3 strains of brusella.
> Thanks
>