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, http://www.bx.psu.edu/miller_lab 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 <inbar.plaschkes@gmail.com> 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: inbar.plaschkes@gmail.com Tel: 08-6479034 054-7915931 Fax: 08-6472983

http://bioinfo.bgu.ac.il

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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: galaxy-user-bounces@lists.bx.psu.edu [galaxy-user-bounces@lists.bx.psu.edu] namens Inbar Plaschkes [inbar.plaschkes@gmail.com] Verzonden: woensdag 13 oktober 2010 11:41 Aan: galaxy-user@bx.psu.edu 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: inbar.plaschkes@gmail.com<mailto:inbar.plaschkes@gmail.com> Tel: 08-6479034 054-7915931 Fax: 08-6472983

http://bioinfo.bgu.ac.il

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Anton Nekrutenko http://nekrut.bx.psu.edu http://usegalaxy.org