[Bioperl-l] please help

[Sean Davis]

On 5/15/06 6:26 AM, "Sean Davis" <sdavis2 at mail.nih.gov> wrote:

> 
> 
> 
> On 5/15/06 4:15 AM, "saurabh maheshwari" <s_maheshwari84 at rediffmail.com>
> wrote:
> 
>>   
>> Hello All
>> I have sent a problem to the earlier also but my problem is still unsolve so
>> i
>> have modified the problem in another way please can any body give me code to
>> make a graph between some items which are in a text file in the following
>> formate:
>> Example
>> item1 interacts with item2 and i want to make graph by giving any item as
>> input and asking all interactions of that item.
>> 
>> item 1      item 2
>> A            B
>> A            C
>> C            B
>> D            B
>> D            E
>> A            F
>> G            A  
> 
> Not a bioperl answer, but in your case, I would suggest looking at using
> cytoscape to do this.  Look here for details:
> 
> http://www.cytoscape.org/

I forgot to mention, if you are looking for a perl solution, I would look at
the Graph module.

http://search.cpan.org/~jhi/Graph-0.69/lib/Graph.pod

You can create the graph according to the docs and then use the neighbors()
method (if I remember correctly) to get the nodes connected to the query
node.

Sean