[Biojava-l] BLAST Networking Questions

[Matthew Pocock]

Vijay Narayanasamy wrote:

> Dear all,
>
>         I'm playing with the following project thru this weekend. I would
> like to do the following. I guess some one would have done this or know this
> already.
>
> I would like to do the following:
>
> 1. Get the sequence data from the user with a GUI.

There is a demo called seqviewer.EmblViewer that is a crude example of how to
build a simple sequence GUI. You should be able to pull out the bits of this
that you need - sequence loading, feature rendering, scaleing etc.

>
> 2. Send the sequence to the BLAST NCBI server

Nancy covered this...

>
>
> 3. Get the output from the server
>

and this.

>
> 4. Present the output (may be in a different form) to the user.

You can use org.biojava.bio.program.sax.BlastLikeSAXParser to parse the
resulting text into usefull information. You could then build new features on
the query sequence (and update the viewer with them), or spit out the hits in
some text format, or whatever.

Good luck

Matthew

>
>
> So the questions are , how to connect with the BLAST server and how to input
> the data in the appropriate database search?
>
> Is it possible to do with Java Servlets? If so how? Any other suggestions or
> comments?
>
> Sincerely,
>
> Vijay
>
> nvijay@psu.edu
>
> http://www.personal.psu.edu/vxn115