[Biojava-l] Using the Meme class

[mark.schreiber at novartis.com]

i think the input stream should be reading the output file of Meme.

- Mark





Te-yuan Chyou <chyte374 at student.otago.ac.nz>
Sent by: biojava-l-bounces at portal.open-bio.org
11/24/2005 06:24 PM

 
        To:     biojava-l at biojava.org
        cc:     (bcc: Mark Schreiber/GP/Novartis)
        Subject:        [Biojava-l] Using the Meme class


Hi,

I'm trying to use the Meme class in org.biojava.bio.program. Currently I
write an application that will perform Meme analysis (to find conserved
motifs in DNA). I had written the application such that it will read a
fasta format file containing multiple fasta sequences. It runs fine but
the "public List getSeqIDs()" and "public List getMotifs()" is producing
empty lists.

While the API of the Meme class does not contain much information (sorry
about the complain), so I'm not sure about how to use the "InputStream is"
parameter of the Meme constructor. Currently I use

InputStream is = new BufferedInputStream(new
FileInputStream("trialSeqs.fa"));

Is it the correct InputStream object?

An example code of perform Meme analysis will also be appreciated
(currently it is not in the tutorial or the cookbook).

Thanks

Te-yuan (David) Chyou

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