[Biojava-l] Collections of sequences

[David Waring]

I will be writing programs that deal will collections of sequences, either
transient or static. I would not modifying the collection in any permantent
sense just working with the collection. I am trying to figure out whether
the SequenceDB interface is the place to start or is there another set of
interfaces/classes geared toward this purpose.

I'll get specific. I want to write something that will run cross_match (or
some other variant of SW) on two collections of sequences. One collection
may be a group of contigs in a sequencing project. These could come from an
an ace file (phrap output) but my program could be dynamicly changing this
collection. The other would be a fasta file with vector sequences.  I then
want to pass these off to my cross_matcher class to compare them and give me
back the results. So I am thinking of extending AbstractSequenceDB to handle
this with different subclasses for different types of sequences. I want to
write the cross_matcher so that it will take two collections of various
types. Does this seem like an appropriate use of SequenceDB?

David

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|   David Waring
|   Systems Programmer
|   University of Washington Genome Center
|   dwaring@u.washington.edu
|   (206) 221-6902
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