Question: reference genome alignment
0
gravatar for wang.yiguan
2.2 years ago by
wang.yiguan30
wang.yiguan30 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 • 1.1k views
ADD COMMENTlink modified 21 months ago by madzayasodara0 • written 2.2 years ago by wang.yiguan30
2
gravatar for urjaswita
2.2 years ago by
urjaswita90
United States
urjaswita90 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 2.2 years ago by urjaswita90

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 2.2 years ago by wang.yiguan30
1
gravatar for a.alsayed.phd
2.2 years ago by
a.alsayed.phd10 wrote:

MSA using DNASTAR lasergene software is one option

ADD COMMENTlink written 2.2 years ago by a.alsayed.phd10
0
gravatar for madzayasodara
21 months ago by
madzayasodara0 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 Like, I have a songbird genome ensemble still unpublished from a collaborator.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 COMMENTlink written 21 months ago by madzayasodara0
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