<p>I'm blasting+ (blastn+ or tblastn) an annotated sequence (a Genbank.xml sequence (nucleotide or protein) or an Uniprot.xml entry) against a DNA database.</p>

<p>Is there a standard tool to map the <strong>features</strong> of the query to the hit ? The best output would be a BED file.</p>

<p>Thanks.</p>

<p>I've answered my own question on my blog: <a href='http://plindenbaum.blogspot.fr/2013/07/mapping-annotations-of-query-sequence.html'>http://plindenbaum.blogspot.fr/2013/07/mapping-annotations-of-query-sequence.html</a></p>

<pre><code>$ java -jar dist/blastmapannots.jar I=P04514.xml B=blast_P04514_vs_AY065842.xml

AY065842    25    961    Non-structural_protein_3    943    +    25961    255,255,255    1    936    25
AY065842    34    469    RNA-binding    970    +    34    469    255,255,255    1    435    34
AY065842    472    640    Dimerization    947    +    472    640    255,255,255    1    168    472
AY065842    532    724    Interaction_with_ZC3H7B    917    +    532    724    255,255,255    1    192    532
AY065842    646    961    Interaction_with_EIF4G1    905    +    646    961    255,255,255    1    315    646
AY065842    520    733    coiled-coil_region    916    +    520    733    255,255,255    1    213    520
</code></pre>
