Have a look at Mark's Biojava in Anger book: http://www.biojava.org/docs/bj_in_anger/
Particularly this bit: http://www.biojava.org/docs/bj_in_anger/ReadFasta.htm This second link has two examples. One reads a fasta file and stores it as a SequenceDB object, the other stores it as a SequenceIterator object. You can get a SequenceIterator object from a SequenceDB by calling db.getSequenceIterator() (assuming your SequenceDB object is called db). Once you have a SequenceIterator you use it like this (assuming the instance of this object is called si) to iterate over the sequences in the file: while (si.hasNext()) { Sequence s = (Sequence)s.next(); // Do stuff with each sequence s here } The Sequence object has methods for getting the name, sequence (represented as a SymbolList object) etc. - look it up in the BioJava Javadocs at http://www.biojava.org/docs/api/ cheers, Richard Richard Holland Bioinformatics Specialist GIS extension 8199 --------------------------------------------- This email is confidential and may be privileged. If you are not the intended recipient, please delete it and notify us immediately. Please do not copy or use it for any purpose, or disclose its content to any other person. Thank you. --------------------------------------------- > -----Original Message----- > From: [EMAIL PROTECTED] > [mailto:[EMAIL PROTECTED] On Behalf Of > Andrea Girardi > Sent: Monday, May 02, 2005 11:15 PM > To: biojava-l@biojava.org > Subject: [Biojava-l] Fasta File > > > Hi to all > > i'm new on this newsletter. I've a problem with Fasta file. I've > downloaded today the BioJava libs and I'd like to know if > there are some > metods to open a fasta file like this: > > >gi|5713315|ref|NP_002060.1| (NM_002069) guanine nucleotide binding > protein (G protein), alpha inhibiting activity polypeptide 1 [Homo > sapiens]gi|12733317|ref|XP_011603.1| (XM_011603) > hypothetical protein > XP_011603 [Homo sapiens]gi|14749912|ref|XP_034149.1| (XM_034149) > guanine nucleotide binding protein (G protein), alpha inhibiting > activity polypeptide 1 [Homo sapiens]gi|121019|sp|P04898|GBI1_HUMAN > GUANINE NUCLEOTIDE-BINDING PROTEIN G(I), ALPHA-1 SUBUNIT (ADENYLATE > CYCLASE-INHIBITING G ALPHA PROTEIN)gi|71892|pir||RGBOI1 GTP-binding > regulatory protein Gi alpha-1 chain (adenylate cyclase-inhibiting) - > bovinegi|2144867|pir||RGHUI1 GTP-binding regulatory protein > Gi alpha-1 > chain (adenylate cyclase-inhibiting) - humangi|391|emb|CAA27288.1| > (X03642) alpha-subunit [Bos taurus]gi|3005737|gb|AAC09361.1| > (AF055013) > guanine nucleotide-binding protein alpha-i subunit [Homo > sapiens]gi|224920|prf||1204197A protein Gi alpha [Bos taurus] > MGCTLSAEDKAAVERSKMIDRNLREDGEKAAREVKLLLLGAGESGKSTIVKQMKIIHEAGYS > EEECKQYKAVVYSNTIQS > IIAIIRAMGRLKIDFGDSARADDARQLFVLAGAAEEGFMTAELAGVIKRLWKDSGVQACFNR > SREYQLNDSAAYYLNDLD > RIAQPNYIPTQQDVLRTRVKTTGIVETHFTFKDLHFKMFDVGGQRSERKKWIHCFEGVTAII > FCVALSDYDLVLAEDEEM > NRMHESMKLFDSICNNKWFTDTSIILFLNKKDLFEEKIKKSPLTICYPEYAGSNTYEEAAAY > IQCQFEDLNKRKDTKEIY > THFTCATDTKNVQFVFDAVTDVIIKNNLKDCGLF > > I've to compare this string with a string in a XML file like this. > > <?xml version="1.0"?> > <sequestresults xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"; > xsi:noNamespaceSchemaLocation="schema1.xsd"> > <origfilename></origfilename> > <origfilepath>D:\sequest\Emoclot_1\Fattore_Ottavo_06_E5\03\</o > rigfilepath> > <bioworksinfo>3.1 SR1</bioworksinfo> > <protein> > <score>1070.4</score> > <accession>4507907</accession> > <peptide> > <file>Fattore_Ottavo_E5_02_001,493-495</file> > <sequence>R.ILAGPAGDSNVVK.L</sequence> > <mass>1241.419</mass> > <charge>2</charge> > <xcorr>2.947</xcorr> > <deltacn>0.048</deltacn> > <sp>865.5</sp> > <rsp>1</rsp> > <ions>16/24</ions> > <count>1</count> > </peptide> > <xpress></xpress> > </peptide> > > Someone can help me? > Thanks, > > Andrea > University of Verona, Italy > > > > _______________________________________________ > Biojava-l mailing list - Biojava-l@biojava.org > http://biojava.org/mailman/listinfo/biojava-l > _______________________________________________ Biojava-l mailing list - Biojava-l@biojava.org http://biojava.org/mailman/listinfo/biojava-l
