[Biojava-l] Multiple questions

Richard HOLLAND hollandr at gis.a-star.edu.sg
Mon Nov 28 20:52:09 EST 2005

Hello Ola,

> 1) Is it possible to search the Biojava-l archives without having to
> manually browse by month?

Not that I know of. Google is a pretty good alternative as it has
indexed all the archive - just add +"biojava-l" to the beginning of your
> 2) Is there a wrapper for SequenceIO.fileToBiojava(..) that
> automatically detects file formats or is it necessary to distinguish
> sequence formats externally, i.e. with different 
> file-extensions? If so,
> does anyone know of a complete list of file-extensions that could be
> mapped to a format?

Yes, there is, but it's not very good and will soon be deprecated.
Programs really should know what they are expecting to read and complain
if they don't find it.
> 3) How robust are the I/O-classes for different formats? The
> test-library provided is rather short in my opinion and my first test
> broke since there was a space in the wrong position...

Depends on the format. In the case of GenBank and EMBL, they are very
stringent about indent sizes because the parsers rely on indents to
identify sections of the files. Different size indents mean different
things. However elsewhere extra spaces should not be a problem. I
haven't really tried that hard yet to break them so don't know exactly.

Incidentally the org.biojavax packages provide a whole new set of
parsers and an updated object model for storing the information that has
been loaded. See the DocBook-format documentation under
"docs/docbook/BioJavaX.xml" in the biojava-live CVS repository. The
comments above refer to these new parsers. The old (1.4) ones really
should not be relied upon for detailed work.
> 4) What are the capabilities for multiple sequence alignment in
> Is it limited to parse results into Biojava objects (as in > BIA) or
> it contain any stable MSA-implementations? Due to BioJavas size it is
> not easy to get an overview of the current capabilities and 
> the standard of different parts.

It can only read alignments. As yet it cannot generate any itself.

> 5) As a novice, has anyone implemented BLAST or CLUSTALW in Java? Any
> public web-services running for this?

Not that I know of. Blast works very well as an external process fired
off by Java and with standard output piped directly back into Java. I
can't see the reason why you'd want to re-implement it unless some
significant change to the algorithm made it necessary. ClustalW
> 6) Is there some example-code on how to use DAS (as a client)?

Don't know.
> 7) How can I submit an RFE?

For now, send it to this list.
Thanks for the interest anyhow - sorry I couldn't answer all your
questions at once! I can definitely recommend investigating the newer
bits of BioJava though (BioJavaX), although they won't officially be
part of it until the 1.5 release, and no date has been set for that yet.


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