[Biojava-l] Fasta File

[Andrea Girardi]

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) - 
bovine
gi|2144867|pir||RGHUI1 GTP-binding regulatory protein Gi alpha-1 
chain (adenylate cyclase-inhibiting) - human
gi|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]
MGCTLSAEDKAAVERSKMIDRNLREDGEKAAREVKLLLLGAGESGKSTIVKQMKIIHEAGYSEEECKQYKAVVYSNTIQS
IIAIIRAMGRLKIDFGDSARADDARQLFVLAGAAEEGFMTAELAGVIKRLWKDSGVQACFNRSREYQLNDSAAYYLNDLD
RIAQPNYIPTQQDVLRTRVKTTGIVETHFTFKDLHFKMFDVGGQRSERKKWIHCFEGVTAIIFCVALSDYDLVLAEDEEM
NRMHESMKLFDSICNNKWFTDTSIILFLNKKDLFEEKIKKSPLTICYPEYAGSNTYEEAAAYIQCQFEDLNKRKDTKEIY
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\</origfilepath>
<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