[BiO BB] aligment of large sequences

[Maximilian Haeussler]

UCSC is using Blastz for the actual alignment and TBA for the postprocessing.

http://www.bx.psu.edu/miller_lab/

Max

On 03/02/06, 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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--
Maximilian Haeussler,
CNRS Gif-sur-Yvette, Paris
tel: +33 6 12 82 76 16
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