Multiz multiple alignment

[femi abiodun elegbeleye]

Hello everyone,

I have gotten local alignments by using Blastz, then how to get a multiple alignment with Multiz and what's the command.

For example , I use Blastz to align A and B and get AB.maf.
Then I use Blastz again to align A and C and get AC.maf.

How can I use these results AB.maf and AC.maf to get a multiple alignment with Multiz?

A step by step work-flow will be highly appreciated. 

Thank you in advance for your help.

Regards,

Femi

[Cath Tyner]

Hello Femi,

Thank you for contacting the UCSC Genome Browser support team and asking this follow-up question to your previously-answered question about creating multiple alignments with the subject line "Research purposes" answered by my colleague, Matt Speir. 

Please review this wiki page for more information: http://genomewiki.ucsc.edu/index.php/Whole_genome_alignment_howto

Also, please note that this resource is a bit outdated in saying that we use blastz. Instead, we use lastz, an improved drop-in replacement for blastz. 

This support team is specifically for UCSC Genome Browser support, and we don't have the resources to provide specific help on generating alignments from tools that are not written by our group. You may be able to find additional support with the resources below:

Multiz and TBA (Threaded-Blockset Aligner) papers:

http://www.bx.psu.edu/miller_lab/dist/tba_howto.pdf

http://pipmaker.bx.psu.edu/dist/tba.pdf

A Practical Guide to Using TBA (see 3.2, "Creating the multiple alignment")

https://www.bx.psu.edu/miller_lab/dist/tba_howto.pdf

Aligning Multiple Genomic Sequences With the Threaded Blockset Aligner

http://genome.cshlp.org/content/14/4/708.full

Biostars

Question: Programming Challange: Pairwise Alignments To Multiple Alignment

https://www.biostars.org/p/2882/

Question: How to construct multiple sequence alignment from group of pairwise alignments

https://www.biostars.org/p/232315/

Please respond to this list if you have further questions!

Thank you for contacting the UCSC Genome Browser support team. 

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Cath
. . .

Cath Tyner

UCSC Genome Browser, Software QA & User Support

UC Santa Cruz Genomics Institute

UCSC Genome Browser

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