[Biojava-l] Vector Trimming in EST's

[David Huen]

On Fri, 22 Jun 2001, Suryavas .K wrote:

> hi everybody
> 
>     I am unable to locate relavent package in BioJava
> for Vector Trimming. pls give me an idea for how to

There isn't one specific to it or even close to it to the best of my
knowledge.

Biojava, being open source software, tends to scratch the itch of those
who write it and directed toward the problems they are solving.  So you
see stuff directed toward external tool searches (CAT's itch),
representation of sequences and features (a Sanger/EBI itch?) but not
stuff for easily generating restriction sites searches, sequence editors,
etc.  You may find the latter and itch you may wish to scratch, in which
case you might consider writing some generalised tool for those purposes.
 

> aproach vector trimming in BioJava packages.
> 
Perhaps you might want to run Blast (or whatever your favourite alignment
poison) searches against a collection of vector sequences and parse the
results.

Or perhaps use the dynamic programming package to implement a little
aligner to match against a specific vector sequence (you usually know the
vector already for any given EST collection.  In fact you only need the
region around the polylinker in many cases).

I might be wrong but neither are likely to be an evening's work.

I think you'll have to read the Javadocs and the sources of the demos
to figure it out.... and perhaps attend a Biojava bootcamp when they hold
it next.

Regards,
David Huen