Hi -
I'm not too familiar with what you are trying to do but...
A lot of the biojava Alignment API can be found in org.biojava.bio.alignment parsers
for reading and writing different formats are in org.biojava.bio.seq.io.* SeqIOTools
is especially useful.
Hope this helps:
- Mark
-----Original Message-----
From: Gabriel del Rio Guerra [mailto:[EMAIL PROTECTED]
Sent: Thu 11/09/2003 4:06 a.m.
To: [EMAIL PROTECTED]
Cc:
Subject: [Biojava-l] Reformating multiple sequence alignments
Hi,
I am interesting in using or developing a program to inter-convert
different sequence alignments formats. In particular I want to translate
HSSP alignments into MSF format. Does anyone knows if this is possible
with Biojava at this point?
Thanks,
Gabriel
-----Original Message-----
From: Kenny Yu [mailto:[EMAIL PROTECTED]
Sent: Wednesday, April 30, 2003 8:45 AM
To: [EMAIL PROTECTED]
Subject: [Biojava-l] unified consolidated annotation system
Both biosql and biodas are concerned with retrieving annotation on the
basis of known features. They are not optimized for large-scale
cross-system queries and data mining on the basis of annotations. I am
interested in consolidating annotations from various sources (such as
genbank and unigene) into a unified form on which I can run queries like
"find features that are linked to DNA repair function in human but not
in mouse" and "find feature whose molecular functions overlap with
those of Accession Number nnnn". Similar mechanisms may exist in LION's
SRS (http://www.lionbioscience.com/solutions/products/srs/relational).
What I am contemplating is essentially a data warehouse for annotations.
I'll borrow data warehouse and OLAP techniques in the design. It's a
hybrid of relational, nested-relational and multidimensional database.
Feature entity, or gene, and annotation are the dimensions. It models
textual values as well as binary objects such as pathway diagrams as
annot!
ation values. I intend to make my work open-source and would call it
UCAsql. Currently the schema design, with some documentation and java
API, is available to anyone upon request by email to myself at
[EMAIL PROTECTED]
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