[Biojava-l] Reformating multiple sequence alignments

[Schreiber, Mark]

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:gdelrio at buckinstitute.org] 
	Sent: Thu 11/09/2003 4:06 a.m. 
	To: biojava-l at biojava.org 
	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:kyu at biodiscovery.com]
	Sent: Wednesday, April 30, 2003 8:45 AM
	To: biojava-l at biojava.org
	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
	kyu at biodiscovery.com.
	
	_______________________________________________
	Biojava-l mailing list  -  Biojava-l at biojava.org
	http://biojava.org/mailman/listinfo/biojava-l
	
	_______________________________________________
	Biojava-l mailing list  -  Biojava-l at biojava.org
	http://biojava.org/mailman/listinfo/biojava-l
	


=======================================================================
Attention: The information contained in this message and/or attachments
from AgResearch Limited is intended only for the persons or entities
to which it is addressed and may contain confidential and/or privileged
material. Any review, retransmission, dissemination or other use of, or
taking of any action in reliance upon, this information by persons or
entities other than the intended recipients is prohibited by AgResearch
Limited. If you have received this message in error, please notify the
sender immediately.
=======================================================================