gene-id by chromosomal location (in JAVA)

View: New views

2 Messages — Rating Filter: Alert me

gene-id by chromosomal location (in JAVA)

by Bernd Jagla-2 :: Rate this Message:

Reply to Author | View Threaded | Show Only this Message

Some parts of this message have been removed. Learn more about Nabble's security policy.

Hello,

I have the following information:

1. Reference genome is from UCSC

2. species is mouse

3. position is on chromosome 2

4. at position 200,000-200,010

5. in forward direction

Now my questions:

What is the gene/CDS that is closest upstream/downstream of this position with the same or different strandness?

(Actually this is many questions in one)

Or is this region in a CDS or intron (strandness?)

I would have to incorporate this in a Java program as a function. (I am trying to avoid anything “Perl+Java” related, and I really have to use JAVA)

How would you go about this?

My suggestion: Load annotation etc into Gbrowse, and access through DAS.

But, I don’t know much about DAS and especially not Java/DAS. Does anyone have any pointer on where to start looking?

Thanks a lot,

Bernd

------------------------------------------------------------------------------
Come build with us! The BlackBerry(R) Developer Conference in SF, CA
is the only developer event you need to attend this year. Jumpstart your
developing skills, take BlackBerry mobile applications to market and stay
ahead of the curve. Join us from November 9 - 12, 2009. Register now!
http://p.sf.net/sfu/devconference
_______________________________________________
Gmod-gbrowse mailing list
Gmod-gbrowse@...
https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse

Re: gene-id by chromosomal location (in JAVA)

by Dave Clements, GMOD Help Desk-2 :: Rate this Message:

Reply to Author | View Threaded | Show Only this Message

Hi Bernd,

First, sorry for not responding sooner. Last week was busy for several of us.

DAS and Java are not my areas of expertise, but some things to look at:

DASOBERT, http://www.spice-3d.org/dasobert/
This is a Java DAS client library.

DASher, http://dasher.sbc.su.se/
DAS client tweaked for proteins.

SPICE: http://www.efamily.org.uk/software/dasclients/spice/
Another DAS client.

I, unfortunately, have no recommendations on which one might be good
to pilfer for classes.

Also:

MyDas, http://code.google.com/p/mydas/
Dazzle, http://www.biojava.org/wiki/Dazzle
These are both Java DAS servers, but may (or may not :-/ ) have some
useful classes for use in a client.

Dave C.

On Fri, Oct 23, 2009 at 6:16 AM, Bernd Jagla <bernd.jagla@...> wrote:

> Hello,
>
>
>
> I have the following information:
>
> 1. Reference genome is from UCSC
>
> 2. species is mouse
>
> 3. position is on chromosome 2
>
> 4. at position 200,000-200,010
>
> 5. in forward direction
>
>
>
> Now my questions:
>
> What is the gene/CDS that is closest upstream/downstream of this position
> with the same or different strandness?
>
> (Actually this is many questions in one)
>
> Or is this region in a CDS or intron (strandness?)
>
>
>
> I would have to incorporate this in a Java program as a function. (I am
> trying to avoid anything “Perl+Java” related, and I really have to use JAVA)
>
>
>
> How would you go about this?
>
>
>
> My suggestion: Load annotation etc into Gbrowse, and access through DAS.
>
> But, I don’t know much about DAS and especially not Java/DAS. Does anyone
> have any pointer on where to start looking?
>
>
>
> Thanks a lot,
>
>
>
> Bernd
>
> ------------------------------------------------------------------------------
> Come build with us! The BlackBerry(R) Developer Conference in SF, CA
> is the only developer event you need to attend this year. Jumpstart your
> developing skills, take BlackBerry mobile applications to market and stay
> ahead of the curve. Join us from November 9 - 12, 2009. Register now!
> http://p.sf.net/sfu/devconference
> _______________________________________________
> Gmod-gbrowse mailing list
> Gmod-gbrowse@...
> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
>
>

--
Please keep responses on the list!
http://gmod.org/wiki/GMOD_News
http://gmod.org/wiki/Training_and_Outreach#Online_Tutorials
Was this helpful? http://gmod.org/wiki/Help_Desk_Feedback

------------------------------------------------------------------------------
Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day
trial. Simplify your report design, integration and deployment - and focus on
what you do best, core application coding. Discover what's new with
Crystal Reports now. http://p.sf.net/sfu/bobj-july
_______________________________________________
Gmod-gbrowse mailing list
Gmod-gbrowse@...
https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse