LastZ on galaxy

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LastZ on galaxy

Inbar Plaschkes
Dear galaxy team,
I would like to know whether it is possible to perform LastZ (multiple sequence alignment tool for aligning different genomes to each other) ?
if so then how ? is there a tutorial you can refer me to ?
many thanks
Inbar 

--
______________________________________________________________
Inbar Plaschkes
Bioinformatics Core Facility
National Institute for Biotechnology in the Negev
Building 51, room 314
Ben-Gurion University of the Negev
Beer-Sheva 84105, Israel
 
Email: [hidden email]
Tel: 08-6479034 054-7915931
Fax: 08-6472983
 
http://bioinfo.bgu.ac.il

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Re: LastZ on galaxy

Abhay Krishna
Yes Lastz is available for NGS Roche 454 platform in stable version of Galaxy
whether it is still available for generic multiple sequence alignment, I dont know.

Abhay



On 13 October 2010 11:41, Inbar Plaschkes <[hidden email]> wrote:
Dear galaxy team,
I would like to know whether it is possible to perform LastZ (multiple sequence alignment tool for aligning different genomes to each other) ?
if so then how ? is there a tutorial you can refer me to ?
many thanks
Inbar 

--
______________________________________________________________
Inbar Plaschkes
Bioinformatics Core Facility
National Institute for Biotechnology in the Negev
Building 51, room 314
Ben-Gurion University of the Negev
Beer-Sheva 84105, Israel
 
Email: [hidden email]
Tel: 08-6479034 054-7915931
Fax: 08-6472983
 
http://bioinfo.bgu.ac.il

_______________________________________________
galaxy-user mailing list
[hidden email]
http://lists.bx.psu.edu/listinfo/galaxy-user



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Re: LastZ on galaxy

Bob Harris
Howdy,

Lastz is available on galaxy but configured for mapping of Roche 454 short reads.  It's not appropriate to use that interface for whole genome alignment.

You probably already know this, but lastz can be found at the Miller Lab webpage,
as the third item under "Software".  There is also a link from there to documentation.

One further point... Inbar refers to lastz as a "multiple sequence alignment tool".  This is not correct, it is purely a pairwise aligner.  For multiple sequence alignment you could use multiz or TBA, which are also available at the Miller Lab webpage.

Bob H


On Oct 13, 2010, at 6:28 AM, Abhay Krishna wrote:

Yes Lastz is available for NGS Roche 454 platform in stable version of Galaxy
whether it is still available for generic multiple sequence alignment, I dont know.

Abhay



On 13 October 2010 11:41, Inbar Plaschkes <[hidden email]> wrote:
Dear galaxy team,
I would like to know whether it is possible to perform LastZ (multiple sequence alignment tool for aligning different genomes to each other) ?
if so then how ? is there a tutorial you can refer me to ?
many thanks
Inbar 

--
______________________________________________________________
Inbar Plaschkes
Bioinformatics Core Facility
National Institute for Biotechnology in the Negev
Building 51, room 314
Ben-Gurion University of the Negev
Beer-Sheva 84105, Israel
 
Email: [hidden email]
Tel: 08-6479034 054-7915931
Fax: 08-6472983
 
http://bioinfo.bgu.ac.il

_______________________________________________
galaxy-user mailing list
[hidden email]
http://lists.bx.psu.edu/listinfo/galaxy-user


_______________________________________________
galaxy-user mailing list
[hidden email]
http://lists.bx.psu.edu/listinfo/galaxy-user


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Re: LastZ on galaxy

Bossers, Alex
In reply to this post by Inbar Plaschkes
Inbar,
as mentioned by others, the lastZ is a pairwise aligner. We have made some (very basic) wrappers for MUMmer (both nucmer and promer as well as mummerplot) which is also a (fast) multi sequence (but still pairwaise) aligner.
http://mummer.sourceforge.net/
Our wrappers are very basic and simple and only intended to have a quicky access to MUMmer from galaxy. We will also post these shortly on the tools sections. After testing cycles have been added.
For beta testing, if you have interest, drop me a pm.

Cheers
Alex

________________________________
Van: [hidden email] [[hidden email]] namens Inbar Plaschkes [[hidden email]]
Verzonden: woensdag 13 oktober 2010 11:41
Aan: [hidden email]
Onderwerp: [galaxy-user] LastZ on galaxy

Dear galaxy team,
I would like to know whether it is possible to perform LastZ (multiple sequence alignment tool for aligning different genomes to each other) ?
if so then how ? is there a tutorial you can refer me to ?
many thanks
Inbar

--
______________________________________________________________
Inbar Plaschkes
Bioinformatics Core Facility
National Institute for Biotechnology in the Negev
Building 51, room 314
Ben-Gurion University of the Negev
Beer-Sheva 84105, Israel

Email: [hidden email]<mailto:[hidden email]>
Tel: 08-6479034 054-7915931
Fax: 08-6472983

http://bioinfo.bgu.ac.il


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Re: LastZ on galaxy

Anton Nekrutenko
Alex:

Would you be willing depositing the wrapper to our tool shed at http://community.g2.bx.psu.edu/.

Thanks!

anton


On Oct 13, 2010, at 9:54 AM, Bossers, Alex wrote:

Inbar,
as mentioned by others, the lastZ is a pairwise aligner. We have made some (very basic) wrappers for MUMmer (both nucmer and promer as well as mummerplot) which is also a (fast) multi sequence (but still pairwaise) aligner.
http://mummer.sourceforge.net/
Our wrappers are very basic and simple and only intended to have a quicky access to MUMmer from galaxy. We will also post these shortly on the tools sections. After testing cycles have been added.
For beta testing, if you have interest, drop me a pm.

Cheers
Alex

________________________________
Van: [hidden email] [[hidden email]] namens Inbar Plaschkes [[hidden email]]
Verzonden: woensdag 13 oktober 2010 11:41
Aan: [hidden email]
Onderwerp: [galaxy-user] LastZ on galaxy

Dear galaxy team,
I would like to know whether it is possible to perform LastZ (multiple sequence alignment tool for aligning different genomes to each other) ?
if so then how ? is there a tutorial you can refer me to ?
many thanks
Inbar

--
______________________________________________________________
Inbar Plaschkes
Bioinformatics Core Facility
National Institute for Biotechnology in the Negev
Building 51, room 314
Ben-Gurion University of the Negev
Beer-Sheva 84105, Israel

Email: [hidden email]<mailto:[hidden email]>
Tel: 08-6479034 054-7915931
Fax: 08-6472983

http://bioinfo.bgu.ac.il


_______________________________________________
galaxy-user mailing list
[hidden email]
http://lists.bx.psu.edu/listinfo/galaxy-user



_______________________________________________
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[hidden email]
http://lists.bx.psu.edu/listinfo/galaxy-user