Question: Which Genome Synteny Program?
3
gravatar for jomaco
6.8 years ago by
jomaco190
European Union
jomaco190 wrote:

Hi,

I'm interested in producing an image similar to figure 1 in this paper: http://www.nature.com/nature/journal/v461/n7262/full/nature08358.html#a2

Can anyone identify the program which may have been used to make this, or a program capable of producing a very similar image?

Although I have found a number of programs, I am not sure if any of them are capable of producing a publication quality figure.

Thanks,

Jom

genome • 5.5k views
ADD COMMENTlink modified 4.4 years ago by Biostar ♦♦ 20 • written 6.8 years ago by jomaco190
5
gravatar for Neilfws
6.8 years ago by
Neilfws48k
Sydney, Australia
Neilfws48k wrote:

From the acknowledgements section of that paper:

We thank [...] J. Crabtree for providing a Sybil (http://sybil.sf.net) software component used to render genome comparison illustrations

Link to software.

ADD COMMENTlink modified 6.8 years ago • written 6.8 years ago by Neilfws48k
1
gravatar for Zev.Kronenberg
6.8 years ago by
United States
Zev.Kronenberg11k wrote:

my pipeline is: running lastz -> circos.

ADD COMMENTlink written 6.8 years ago by Zev.Kronenberg11k

Hi Zev,

I am using the USCS Lastz pipeline, however, I would now like to visualize my MAF file on circos. Do you have a pipeline on how to visualize the multiple alignment file on Circos? Please let me know. Thank you

ADD REPLYlink modified 8 months ago by RamRS27k • written 4.8 years ago by chitoboy0

I just re-format the tabular output option of lastZ into the link format for circos. 

ADD REPLYlink written 4.8 years ago by Zev.Kronenberg11k
0
gravatar for Vitis
6.8 years ago by
Vitis2.4k
New York
Vitis2.4k wrote:

Gbrowse_syn could do something similar, but you need to run the whole genome alignment first, which is usually not a trivial task. You could read the 'A Note on Whole Genome Alignments' section at the end of Gbrowse_syn webpage to give it a try. http://www.gmod.org/wiki/GBrowse_syn_Tutorial

ADD COMMENTlink written 6.8 years ago by Vitis2.4k
0
gravatar for gammyknee
6.8 years ago by
gammyknee200
Australia
gammyknee200 wrote:

Isnt exactly the same as that figure but ACT (https://www.sanger.ac.uk/resources/software/act/) will do something fairly similar

ADD COMMENTlink written 6.8 years ago by gammyknee200
0
gravatar for cts
6.8 years ago by
cts1.6k
Pasadena
cts1.6k wrote:

EasyFig can make this sort of image

ADD COMMENTlink written 6.8 years ago by cts1.6k
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