Lastz On Galaxy

Question: Lastz On Galaxy

8.1 years ago by

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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modified 8.1 years ago by Bossers, Alex • 240 • written 8.1 years ago by Inbar Plaschkes • 20

8.1 years ago by

Abhay Krishna • 70

Abhay Krishna • 70 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

ADD COMMENT • link written 8.1 years ago by Abhay Krishna • 70

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

ADD REPLY • link written 8.1 years ago by Bob Harris • 190

8.1 years ago by

Bossers, Alex • 240

Bossers, Alex • 240 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

ADD COMMENT • link written 8.1 years ago by Bossers, Alex • 240

Alex: Would you be willing depositing the wrapper to our tool shed at http://community.g2.bx.psu.edu/. Thanks! anton Anton Nekrutenko http://nekrut.bx.psu.edu http://usegalaxy.org

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