Ikro Once you have that Sequence object you should note that Sequence implements SymbolList. So you can call any of the SymbolList methods on s.
Find the base a position 234 Symbol sym = s.symbolAt(234) Or get the String version of the DNA sequence so you can print it. String myString = s.seqString() Sequence has all the SymbolList function plus much more. > -----Original Message----- > From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED]]On > Behalf Of Schreiber, Mark > Sent: Thursday, April 11, 2002 2:55 PM > To: Ikro Yoon; [EMAIL PROTECTED] > Subject: RE: [Biojava-l] extracting genome sequence from Genbank file > > > Hi - > > The following should do it: > > File gbFile = new File("myGBFile.gbk"); > SequenceIterator si = SeqIOTools.readGenbank( new BufferedReader( > new FileReader(gbFile),1024)); > Sequence s = si.next(); > > This returns a sequence iterator that iterates through all the sequences > in the GenBank file. In most GB files there is only one sequence so you > can get away with one call to si.next(); If there is more than one then > you could do this. > > ArrayList seqs = new ArrayList(); > while(si.hasNext()){ > seqs.add(si.next()); > } > > Or if you want you could use a biojava SeqDB object rather than an array > list. The SeqDB allows you to retreive a specific sequence by ID. > > Mark > > > > -----Original Message----- > > From: Ikro Yoon [mailto:[EMAIL PROTECTED]] > > Sent: Friday, 12 April 2002 9:11 a.m. > > To: [EMAIL PROTECTED] > > Subject: [Biojava-l] extracting genome sequence from Genbank file > > > > > > Hello, > > > > I have just started using biojava and find it extremely useful. > > Particularly, I am using it for parsing Genbank files. I took > > a look at the documentation as well as TestGenbank.java under > > demos/seq directory to get an idea of how to extract various > > information from Genbank files. > > > > One thing that I am still having trouble is extracting the > > genome sequence at the end of Genbank file. How could I do that? > > > > Thank you for your help. > > > > Ikro > > _______________________________________________ > > Biojava-l mailing list - [EMAIL PROTECTED] > > 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. > ======================================================================= > _______________________________________________ > Biojava-l mailing list - [EMAIL PROTECTED] > http://biojava.org/mailman/listinfo/biojava-l _______________________________________________ Biojava-l mailing list - [EMAIL PROTECTED] http://biojava.org/mailman/listinfo/biojava-l
