Drawing A Schematic Genomic Context Tree
4
1
Entering edit mode
8.5 years ago
Iddo ▴ 230

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?

visualization evolution genomics genome • 5.5k views
ADD COMMENT
1
Entering edit mode

what's your input ?

ADD REPLY
0
Entering edit mode

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 REPLY
3
Entering edit mode
8.5 years ago

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 COMMENT
0
Entering edit mode

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

ADD REPLY
1
Entering edit mode

ACN: Accession number

ADD REPLY
1
Entering edit mode

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 REPLY
0
Entering edit mode

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

ADD REPLY
0
Entering edit mode

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

ADD REPLY
1
Entering edit mode
8.5 years ago
Asaf 9.3k

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

ADD COMMENT
0
Entering edit mode

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

ADD REPLY
0
Entering edit mode
8.5 years ago
Mary 11k

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 COMMENT
0
Entering edit mode
8.5 years ago
Fabsta ▴ 120

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 COMMENT

Login before adding your answer.

Traffic: 1514 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6