Wormweb.org: Exon-intron graphic maker and neural network visualization

Hi everyone,

My name is Nikhil Bhatla, and I’m a grad student in the Horvitz lab at MIT. I’ve made a couple of free, web-based tools that I thought others might find interesting and useful. Both of them are available at http://wormweb.org/


  1. Exon-intron Graphic Maker:

Available at: http://wormweb.org/exonintron

This is a tool for quickly making proportional, publication-quality graphics that display your gene’s important parts: 5’ UTR, coding sequence, 3’ UTR, and mutations and deletions. All you need to do is copy and paste your gene’s sequence into the various text boxes, and a preview of the gene’s visualization will be displayed. You can copy and paste gene sequences directly from Wormbase, and it will understand that capitalized letters are exons while lowercase letters are introns. You can also distinguish exons and introns by separating them with commas. After constucting your gene graphic, you can download it as a vectorized PDF. This PDF can then be modified without any loss of quality in a program like Adobe Illustrator.

Hopefully this tool will make gene model creation much less tedious than it currently is! More detailed instructions can be found at http://wormweb.org/exonintron.


  1. Interactive C. elegans Neural Network:

Available at: http://wormweb.org/neuralnet

(Fastest in Google Chrome, Safari, and then Firefox. Doesn’t work in Internet Explorer)

This is a tool that allows you to navigate the C. elegans neural network as described in various papers published over the past ~25 years. I presented a poster on it at the last worm conference in UCLA.

Things you can do with it:
a) Click on neurons to re-center them and see what other neurons they’re connected to

b) Specify a start neuron and an end neuron to find the shortest path between 2 neurons (e.g. ASE [salt sensor] and AVA [command motor neuron])

c) Zoom in and out to view neurons more than just 1-degree away

d) View all connections in the visible portion of the network (makes a dense spiderweb) by checking the “Show more connections on the graph” checkbox

e) View and search the network of individual neurons. By default, neuron groups (e.g. pairs of neurons) are displayed, but this is an oversimplification, and the individual neuron network is a more accurate representation of the true network.

The network includes all 302 neurons and a handful of other cells and cell groups (e.g. muscle). Note that the network can be broken into 2 pieces: the main neural network and the pharyngeal neural network. These networks are thought to be connected by only a single gap junction between RIP (of the main network) and I1 (of the pharyngeal network). Note that 1 other neuron (CAN) is not known to make any synapses to other neurons, so is effectively an island.

More details (including a list of data sources and other technical details): http://wormweb.org/details.html


Let me know if you have any suggestions, ideas, questions or comments about these tools.

I hope you find them useful!

  • nikhil


Loving the Exon-intron Graphic Maker! Two thumbs up!

Unfortunately about a month too late for my thesis, though… ::slight_smile:

Thank you so much Nikhil. :-* Exon-intron Graphic Maker is so useful.
I will try to use it for my thesis which will be submitted in the next 3 months. ;D … :’(

Cool stuff, Nikhil! Love the connectivity browser.

Users might be interested to know the the Genome Browser can also generate publication quality graphics. Simply navigate to a region of interest, select the tracks you wish to include, then select “Hi-resolution image”. This will generate a scalable vector graphics (SVG) file editable in apps like Illustrator.

Can’t donwload the pdf. Anybody knows why?