[Biojava-l] Multiple questions

Ola Spjuth ola.spjuth at farmbio.uu.se
Mon Nov 28 04:54:37 EST 2005


I am investigating the usefulness of BioJava as a backend for sequence
management in Bioclipse (www.bioclipse.net). As a total newbie to
Biojava, I have read the tutorial, BIA examples, glanced at the API,
read my first FASTA-sequence and have come up with a few questions:

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

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?

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...

4) What are the capabilities for multiple sequence alignment in Biojava?
Is it limited to parse results into Biojava objects (as in BIA) or does
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.

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

6) Is there some example-code on how to use DAS (as a client)?

7) How can I submit an RFE?

Sorry for so many questions in one post; I have a lot of catching up to
do and was hoping for some guidance. Some answers have probably already
been answered in earlier posts but I have not been able to search the



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