[Biojava-dev] Local/Global Alognment?

[Thomas Down]

Once upon a time, Vaibhav Agrawal wrote:
> Hi!
> Can i perform Local and Global alognment on nucleotide sequence using
> BioJava classes. I yes, can u plase direct me to some examples.

BioJava includes a dynamic programming toolkit which can certainly
be used to perform nucleotide alignments.  There's a simple
demonstration of this in the BioJava source distribution: look
at the file demos/dp/PairwiseAlignment.java

This demonstration actually runs on protein sequences, but
because BioJava's sequence model is all expressed in terms
of Alphabet and Symbol objects, it should be very easy to
convert it to use the DNA or RNA alphabets (or even do something
a bit more complex, like aligning a DNA sequence to a protein).

There's a nice explanation of the dynamic programming
toolkit at:

    http://www.biojava.org/tutorials/dp-doc.html

This isn't directly related to pairwise alignment, but the
principles (and the APIs) are the same.

There's a nice explanation of the dynamic programming
toolkit at:

    http://www.biojava.org/tutorials/dp-doc.html

This isn't directly related to pairwise alignment, but the
principles (and the APIs) are the same.  There's a lot of
information about sequence alignment and dynamic programming
in the book ``Biological sequence analysis'':

    http://www.amazon.co.uk/exec/obidos/ASIN/0521629713/ref=sr_aps_books_1_1/202-5685863-0143010


Hope this helps,

     Thomas.