[Biojava-l] Using the Meme class

mark.schreiber at novartis.com mark.schreiber at novartis.com
Sun Nov 27 01:54:13 EST 2005

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


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

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).


Te-yuan (David) Chyou

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