Question: Drawing A Schematic Genomic Context Tree
1
gravatar for Iddo
6.4 years ago by
Iddo230
Iddo230 wrote:

Is there any software out there that can draw a simple, schematic rendering of a gene block across multiple species? The result should be something like: http://imgur.com/iKolcBU

Plenty of such renderings in STRING, FIG and EcoCyc, to name those that I know. Anyone has a pointer to a standalone or a web-based program that does this?

ADD COMMENTlink modified 6.4 years ago by Fabsta120 • written 6.4 years ago by Iddo230
1

what's your input ?

ADD REPLYlink written 6.4 years ago by Pierre Lindenbaum129k

I can tailor my input to whatever's appropriate. If I were to write something like that (which seems like I would have to do), my input would be some sort of GFF file.

ADD REPLYlink written 6.4 years ago by Iddo230
3
gravatar for Pierre Lindenbaum
6.4 years ago by
France/Nantes/Institut du Thorax - INSERM UMR1087
Pierre Lindenbaum129k wrote:

I played with that problem and quickly wrote the following program: https://github.com/lindenb/jvarkit/wiki/Biostar95652

It reads a list of protein ACN and ouputs a SVG file:

$ java -jar dist/biostar95652.jar \
   NP_077719.2 \
   XP_513697.3 XP_001114248.1 \
   XP_540266.3 XP_002686160.2 \
   NP_035058.2 NP_077334.1 \
   NP_001238962.1 NP_001108566.1 > result.svg

http://i.imgur.com/SYn6IAal.png

enter image description here

ADD COMMENTlink modified 6.4 years ago • written 6.4 years ago by Pierre Lindenbaum129k

Wow, looks nifty! What's an ACN? Also, how is the tree topology determined?

ADD REPLYlink modified 6.4 years ago • written 6.4 years ago by Iddo230
1

ACN: Accession number

ADD REPLYlink written 6.4 years ago by Pierre Lindenbaum129k
1

My input is a Genbank file. I use the GBSeq_taxonomy field in the Genbank file:

$ curl -s "http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=protein&rettype=gb&retmode=xml&id=NP_001100509.1" | grep GBSeq_taxonomy

<GBSeq_taxonomy>Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Sciurognathi; Muroidea; Muridae; Murinae; Rattus</GBSeq_taxonomy>
ADD REPLYlink modified 6.4 years ago • written 6.4 years ago by Pierre Lindenbaum129k

Nice. So how does this work for multiple genes / organism as in here? (Each arrow is a gene). http://imgur.com/iKolcBU

ADD REPLYlink written 6.4 years ago by Iddo230

I thought the blocks were the domains of one gene :-) I cannot do anything without a valid input file :-)

ADD REPLYlink written 6.4 years ago by Pierre Lindenbaum129k
1
gravatar for Asaf
6.4 years ago by
Asaf8.3k
Israel
Asaf8.3k wrote:

Not exactly what you're looking for but iTOL can produce these figures:
iTOL example

ADD COMMENTlink modified 6.4 years ago • written 6.4 years ago by Asaf8.3k

Can't really see anything there. Anyhow, I thought iTOL only does trees.

ADD REPLYlink written 6.4 years ago by Iddo230
0
gravatar for Mary
6.4 years ago by
Mary11k
Boston MA area
Mary11k wrote:

Could you kludge webgbrowse to make that? http://webgbrowse.cgb.indiana.edu/webgbrowse/glyphdoc.html

I know that's not designed to do multiple species, but it might be possible to get close to what you want by creating different tracks?

ADD COMMENTlink written 6.4 years ago by Mary11k
0
gravatar for Fabsta
6.4 years ago by
Fabsta120
Fabsta120 wrote:

We have a reusable JavaScript tree plugin in the BioJS project.

https://www.ebi.ac.uk/Tools/biojs/registry/Biojs.Tree.html

It uses D3 and a JSON file.

ADD COMMENTlink written 6.4 years ago by Fabsta120
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