[BiO BB] aligment of large sequences

[Boris Steipe]

You could also try LAGAN

http://lagan.stanford.edu/lagan_web/index.shtml

in particular Shuffle_Lagan handles inversions, transpositions(!) and  
even some degree of duplications.

HTH,

B.




On 4 Feb 2006, at 03:15, William Hsiao wrote:

> Hi Renxue,
>    You might want to try http://gel.ahabs.wisc.edu/mauve/
>
> Cheers,
>
> Will
>
> On 2/3/06, Renxue Wang <rwang at bccrc.ca> wrote:
>> Hi, there,
>>
>> Anybody knows any good program for alignment/comparison of large  
>> sequences, e.g., two genomes of closely related species, for  
>> identifying the inversion deletion and translocation.
>>
>> Thanks,
>>
>> Renxue Wang
>>
>> -----Original Message-----
>> From: bio_bulletin_board-bounces+rwang=bccrc.ca at bioinformatics.org  
>> [mailto:bio_bulletin_board-bounces 
>> +rwang=bccrc.ca at bioinformatics.org] On Behalf Of Yaoqi Zhou
>> Sent: Friday, February 03, 2006 5:33 AM
>> To: The general forum at Bioinformatics.Org
>> Subject: Re: [BiO BB] (no subject)
>>
>> The most recent comparison can be found in comparing SPEM with other
>> sequence alignment methods.
>>
>> H. Zhou and Y. Zhou, ``SPEM: Improving multiple-sequence alignment  
>> with
>> sequence profiles and predicted secondary structures'',  
>> Bioinformatics
>> 21, 3615--3621 (2005).
>>
>> Download and/or run SPEM server at http://theory.med.buffalo.edu
>>
>> Yaoqi Zhou, Associate Professor
>> **CHECK out Newly UPDATED webpage** on
>> http://theory.med.buffalo.edu
>> Department of Physiology and Biophysics
>> University at Buffalo, State University of New York
>> 124 Sherman Hall,  Buffalo, NY 14214
>> (716) 829-2985 Fax (716) 829-2344
>> Email: yqzhou at buffalo.edu
>> NEW Office/Lab Address: 306/308 Cary Hall
>>
>> On Feb 2, 2006, at 6:31 PM, Franklin Jose wrote:
>>
>>> Hai everybody
>>> Is there any difference between tools, methods and algorithms in
>>> sequence alignment?
>>>
>>> Franklin
>>> Lecturer
>>> Govt. Arts College
>>> Udhagai-643002
>>>
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>
> --
> William Hsiao
> PhD Student, Brinkman Laboratory
> Department of Molecular Biology and Biochemistry
> Simon Fraser University, 8888 University Dr. Burnaby, BC, Canada  
> V5A 1S6
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