Question: reference genome alignment
0
gravatar for wang.yiguan
13 days 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 • 135 views
ADD COMMENTlink modified 13 days ago by a.alsayed.phd0 • written 13 days ago by wang.yiguan0
1
gravatar for urjaswita
13 days ago by
urjaswita30
United States
urjaswita30 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 13 days ago by urjaswita30

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 11 days ago by wang.yiguan0
0
gravatar for a.alsayed.phd
13 days ago by
a.alsayed.phd0 wrote:

MSA using DNASTAR lasergene software is one option

ADD COMMENTlink written 13 days ago by a.alsayed.phd0
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 839 users visited in the last hour