Question: reference genome alignment
0
gravatar for wang.yiguan
10 weeks ago by
wang.yiguan0 wrote:

Hi, I have a new reference genome. And I intend to align it to reference genome of other related species, so as to determine the ancestral state for our reference genome. It's like genome alignment to genome. which tools can be used to achieve this? Thanks very much.

alignment genome • 199 views
ADD COMMENTlink modified 10 weeks ago by a.alsayed.phd0 • written 10 weeks ago by wang.yiguan0
1
gravatar for urjaswita
10 weeks ago by
urjaswita50
United States
urjaswita50 wrote:

You want to do multiple genome alignments. There are many tools to do that -- MultiZ, and TBA from UCSC and Enredo-Peacan-Ortheus (EPO) from Ensembl are among the broadly used approaches.

You can look at Alignathon paper for many tools and comparisons. http://genome.cshlp.org/content/early/2014/10/01/gr.174920.114

ADD COMMENTlink written 10 weeks ago by urjaswita50

Thanks for your suggestion. I am new to bioinformatics, and the paper does help me a lot in understanding these tools! I am now trying MUMmer, and it seems work for me.

ADD REPLYlink written 10 weeks ago by wang.yiguan0
0
gravatar for a.alsayed.phd
10 weeks ago by
a.alsayed.phd0 wrote:

MSA using DNASTAR lasergene software is one option

ADD COMMENTlink written 10 weeks ago by a.alsayed.phd0
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