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Question: reference genome alignment
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gravatar for wang.yiguan
9 months ago by
wang.yiguan • 10
wang.yiguan • 10 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 • 450 views
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modified 3 months ago by madzayasodara • 0 • written 9 months ago by wang.yiguan • 10
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gravatar for urjaswita
9 months ago by
urjaswita • 70
United States
urjaswita • 70 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 COMMENT • link written 9 months ago by urjaswita • 70

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 REPLY • link written 9 months ago by wang.yiguan • 10
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gravatar for a.alsayed.phd
9 months ago by
a.alsayed.phd • 10
a.alsayed.phd • 10 wrote:

MSA using DNASTAR lasergene software is one option
ADD COMMENT • link written 9 months ago by a.alsayed.phd • 10
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gravatar for madzayasodara
3 months ago by
madzayasodara • 0
madzayasodara • 0 wrote:

Nice! Which one of these tools would allow me to reannotate the aligned genome? Like, I have a songbird genome ensemble still unpublished from a collaborator. This genome was mapped and annotated using a mix of stuff they did there. I want to align the ref falcon genome to this songbird genome and reannotate based on it. So that the positions correspond to each other. Tnxs
ADD COMMENT • link written 3 months ago by madzayasodara • 0
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